Introduction and Acknowledgements

Authors: Andras Lasso (PerkLab, Queen's University), Matt Lougheed (PerkLab, Queen's University)
Contact: Andras Lasso <email>lasso@queensu.ca</email>
Website: http://www.slicerrt.org/
License: Slicer license

Extension Description

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