Documentation/Nightly/Extensions/VolumeClip

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For the stable Slicer documentation, visit the 4.6 page.

Introduction and Acknowledgements

Authors: Andras Lasso (PerkLab, Queen's University), Matt Lougheed (PerkLab, Queen's University)
Contact: Andras Lasso
Website: http://www.slicerrt.org/
License: Slicer license

Extension Description

VolumeClipLogo.png

This extension contains modules for clipping image volumes with arbitrary surfaces or region of interest boxes.

Modules

  • Volume clip with model
    • Removes volume contents inside or outside the selected surface model
    • User may define and dynamically edit a 3D clipping surface by markup points (uses Delaunay triangulation, therefore it mostly generates convex surfaces)
    • For incremental clipping select the input volume also as output volume
  • Volume clip with ROI box
    • Removes volume contents inside or outside the selected region of interest box
    • For incremental clipping select the input volume also as output volume

Use Cases

Remove patient table from CT volumes

  • Go to Volume clip with model module
  • Set:
    • Input volume: your input image
    • Clipping surface: Create new model
    • Clipping surface from markups: Create new MarkupsFiducial
    • Fill value: on CT: -1000 (radiological density of air on CT), on MR: 0 (typical background voxel brightness)
    • Output volume: Create new volume
  • Drop/move a few markup fiducials around your region of interest on a couple of axial slices
  • Click apply

Clip irrelevant image areas of the input volume before segmentation

  • Go to Volume clip with model module
  • Set:
    • Input volume: your input image
    • Clipping surface: Create new model
    • Clipping surface from markups: Create new MarkupsFiducial
    • Clip outside: uncheck
    • Fill value: background voxel value (depending on your imaging modality it may be -1000, 0, or other)
    • Output volume: Create new volume
  • Drop/move a few markup fiducials around the image areas that you would like to remove
  • Click apply
  • If there are more areas to remove then set the created Volume node as Output volume and repeat the following steps
    • Set: Clipping surface from markups: Create new MarkupsFiducial (or go to the Markups module to remove all fiducials from the current list)
    • Drop/move a few markup fiducials around the image areas that you would like to remove
    • Click apply

Create quick mask for registration

  • Go to Volume clip with model module
  • Set:
    • Input volume: your input image
    • Clipping surface: Create new model
    • Clipping surface from markups: Create new MarkupsFiducial
    • Output volume: Create new volume
  • Drop/move a few markup fiducials around your region of interest on 2-3 orthogonal slices (3-4 fiducials on each slice should be enough)
  • Click apply
  • Set:
    • Input volume: Volume (the mask volume that you created)
    • Clip outside: uncheck
    • Fill value: 100
  • Click apply

Tutorials

Short video of volume clipping with model: https://www.youtube.com/watch?v=1mYNwJbE7dQ

Similar Extensions

Documentation/Nightly/Extensions/ModelClip

References

Information for Developers

Source code: https://subversion.assembla.com/svn/slicerrt/trunk/VolumeClip