Documentation/Nightly/Extensions/VolumeClip

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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 Volume clip with model (before clipping) Volume clip with model (after clipping) Volume clip with ROI box 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://github.com/PerkLab/SlicerVolumeClip