Documentation/4.10/Modules/TransformVisualizer

The transform visualization functionality has been merged to the Slicer core (Transforms module, Display section), therefore it is not distributed as a separate extension anymore! See up-to-date information in the Transforms module documentation

For the latest Slicer documentation, visit the read-the-docs.

Introduction and Acknowledgements

This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions. Author: Franklin King (PerkLab, Queen's University) Contributors: Andras Lasso (PerkLab, Queen's University), Csaba Pinter (PerkLab, Queen's University) Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email>

Cancer Care Ontario   Software Platform and Adaptive Radiotherapy Kit   Ontario Consortium for Adaptive Interventions in Radiation Oncology

Module Description

The Transform Visualizer module visualizes transforms using various options. The module can visualize any transform (linear transform, B-spline deformable transform, any other non-linear transform) or vector volume.

Use Cases

• Visualize deformation fields
• Visualize vector volumes
• Visualize transforms

Transform Visualizer module UI with glyph visualization mode active

Transform Visualizer modes

Tutorials

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Panels and their use

• IO
  • Input
    • Deformation: The deformation which will be visualized. The deformation can be represented as either a vector volume or a transform (linear or non-linear) with a reference image.
    • Reference Image: The reference image to be used with a selected transform to generate a deformation field. Enabled only when a transform is selected as the input deformation. The deformation field will be generated when both a valid deformation and a reference image are selected.
  • Output
    • Output Model: A model to be selected or created that will contain the output.

• Visualization Mode
  • Glyph: Generates glyphs oriented to the vector direction and scaled to the vector magnitude
  • Grid: Generates a cube grid that is warped by the deformation field
  • Block: Generates a rectangular model that is then warped by the deformation field
  • Contour: Generates isosurfaces according to the vector magnitudes of the deformation field
  • Glyph Slice: Projects the deformation field to a chosen slice view and generates glyphs oriented to the vector direction and scaled to the vector magnitude
  • Grid Slice: Projects the deformation field to a chosen slice view and generates a cube grid that is warped by the deformation field

• Parameters
  • Glyph Options
    • Number of Glyphs: Number of randomly placed glyphs to create
    • Magnitude Threshold: Only vectors with a magnitude within the specified range will be represented with a glyph
    • Scaling
      • Scale Factor: Multiplier for size of glyph relative to vector magnitude
      • Directional Scaling: Scale glyph only along the vector direction
      • Isotropic Scaling: Scale glyph in all directions
    • Source: Model to be used as the glyph model; arrow, cone, and sphere are available and each have their own respective options
    • Random Seed: Seed used for random placement of glyphs
  • Grid Options
    • Scale Factor: Multiplier for the scale of the deformation
    • Spacing: Line spacing used to generate a cube grid
  • Block Options
    • Scale Factor: Multiplier for the scale of the deformation
  • Contour Options
    • Number of Contours: Number of contours to generate between the specified range values
    • Range: Range to create contours within
    • Decimate: Target decimation as a decimal percentage reduction in polygons (0 results in no decimation whereas 0.99 results in a target of 99% reduction in polygons)
  • Glyph Slice Options
    • Slice: Slice view to orient and project the glyphs to
    • Number of Glyphs: Number of randomly placed glyphs to create in total
    • Magnitude Threshold: Only vectors with a magnitude within the specified range will be represented with a glyph
    • Scale Factor: Multiplier for size of glyph relative to vector magnitude
    • Random Seed: Seed used for random placement of glyphs
  • Grid Slice Options
    • Slice: Slice view to orient and project the glyphs to
    • Scale Factor: Multiplier for size of glyph relative to vector magnitude
    • Spacing: Line spacing used to generate a square grid

Similar Modules

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References

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Information for Developers

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