Difference between revisions of "Documentation/Labs/Segmentations"

From Slicer Wiki
Jump to: navigation, search
Line 95: Line 95:
== Switch between scalar/labelmap volume ==
== Switch between scalar/labelmap volume ==
Previously it was possible to switch between scalar/labelmap type by changing an attribute value. Now scalar/labelmap volumes are stored in different classes, therefore a new node has to be created for the converted volume. Conversion options:
* Use the ''Cast Scalar Volume'' module to convert between scalar/labelmap volumes.
* Create a new node for the target representation and pass the image data of the source node to the target node. For example, conversion to labelmap volume:
    scalarVolume = slicer.util.getNode('MRHead')
See [[Documentation/Nightly/FAQ#How_to_switch_between_scalar.2Flabelmap_volume_.3F]]
    labelVolume = slicer.modules.volumes.logic().CreateAndAddLabelVolume(scalarVolume,scalarVolume.GetName()+'-label')

Revision as of 00:52, 13 November 2015

Home < Documentation < Labs < Segmentations




  • New Segmentation MRML node that can contain multiple segments and multiple representations for segments
  • Automatic conversion between representations
  • Visualization of lablemap and model representations simultaneously in 2D or 3D views
  • Copy/move segments between segmentations
  • Import/export representations into labelmap ormodel nodes
  • Drastic improvement in memory usage compared to labelmaps and conversion speed compared to Contours (the previous SlicerRT mechanism for the same purpose, predecessor of Segmentations) due to only allocating the effective extent

Design and implementation

  • New Segmentation MRML node that can contain multiple segments and multiple representations for all segments
    • Each segment has the same set of representations. This means that if segments are copied/moved between segmentations, then conversion will take place if possible (if not then copy will fail)
    • Supported representations (initially) are
      • Binary lablemap (vtkOrientedImageData)
      • Closed surface (vtkPolyData)
      • Planar contour (vtkPolyData)
    • Additional representations can be added, such as Ribbon model or Fractional labelmap that can be found in SlicerRT
  • Conversion between representations are driven by a conversion graph in which the nodes are the representations and the edges are conversion rules
    • When converting with the default method (Create: 'Default' button), then the path with the lowest cost is used (rules have a cost field that gives a ballpark value for the conversion cost)
Segmentations module, Visualizing model in 2D and 3D, also showing merged labelmap in 2D
Class diagram


Segmentation modules is part of the SlicerRT extension during development and will be moved to Slicer core when the developments are complete:

Slicer core changes


Future features

  • Editor module that can edit segmentation labelmap representations the same way as Editor module currently can
  • CLI support for vtkMRMLSegmentationNode


  • Opacity spinbox does not update until done

Topics to discuss

  • Ability to support potential use cases
    • Huge number of segments vs memory (compressed representation and/or on-demand loading)
    • SceneViews (states are defined basically by display node visibility on/off)
    • FiberTract support
  • Partial SH visibility for segmentation that tracks segment visibility? What happens when the segmentation visibility is set? All show/hide?


vtkMRMLLabelMapVolumeNode integration

Slicer core updated, see this commit: https://github.com/Slicer/Slicer/commit/e4ffa1f6dcfafc1ca8f0015ecf02a0c23a8bd503

Module update instructions

Module selectors that expect a labelmap volume should be changed


   self.outputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
   self.outputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 1)


   self.outputSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]


   self.outputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
   self.outputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0)


   self.outputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
  • Note: This changes the value assigned to nodeTypes from a Tuple with 2 elements to a List with only one element. Additional information on the Tuple syntax can be found here: https://wiki.python.org/moin/TupleSyntax

CLI modules

CLI modules are not impacted. No change is needed in interface definition XML files or in the module implementation.

Switch between scalar/labelmap volume

See Documentation/Nightly/FAQ#How_to_switch_between_scalar.2Flabelmap_volume_.3F