Documentation/Nightly/Modules/LandmarkRegistration

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For the stable Slicer documentation, visit the 4.8 page.


Introduction and Acknowledgements

Information on NA-MIC can be obtained from the NA-MIC website.
Author: Steve Pieper, Isomics, Inc.
Contact: Steve Pieper,

Isomics, Inc.  
NA-MIC  
NAC  

Module Description

Interactive registration and visualization.

LandmarkRegistration Module

Use Cases

Examples:

  • Use Case 1: Interactively align two volumes
  • Use Case 2: Align volumes as pre-processing step for automated registration
  • Use Case 3: Visually review results of automated registration

Tutorials

Panels and their use

When you enter the module it will prompt for a fixed and moving volume. The is trigger the creation of a transformed volume that is a duplicate of the moving volume. Operations will take place on the "-transformed" volume.

  • Parameters: these are the currently selected volumes and can be changed using the "Select Volumes To Register" button.
  • Visualization
    • Layout: by clicking these buttons you can change what orientations are shown by for each volume. The order will always be: Fixed first, Moving in the middle, Fixed plus transform blended last.
    • Display: select which of the volumes to display
    • RevealCursor: creates a 2x2 checkerboard of the bg and fb volumes of a slice view. Follows mouse. Note you can also put label maps in fg layer for inspection.
    • Controls all fixed/moving slice views
      • Rock: goes back and forth between volumes
      • Flicker: flashes between volumes
    • Zoom: synchronous inspection of all slice views
  • Landmarks
    • Add: puts you in landmark placement mode, and any click in fixed or moving will create a landmark in both volumes (corresponding to named fiducial list).
    • Landmarks are monitored so that any movement causes all other viewers to center on that landmark. Moving a landmark can trigger update of the active registration.
  • Registration
    • Registration Type: selects what is active
      • Affine Registration: Supports three modes.
        • Rigid: only rotate, translate
        • Similarity: rigid + uniform scale
        • Affine: rotate, translate, non-uniform scale, non-uniform shear
      • ThinPlate Registration
        • Hot Update: recalculate the nonlinear transform at every mouse movement.
        • Export to Grid Transform: create a transform that can be saved/loaded and used with CLIs (thin plate can be used only within the Landmark Registration module).

Note that these transforms work with the transform visualization modes for real-time visualization.

Similar Modules

Transforms

References

N/A

Information for Developers

This module is written in python. There is a pluggable API for defining new interactive registrations. Implement a subclass of a RegistrationPlugin in python. It can call C++ routines either wrapped in VTK, through SimpleITK, or by calling a CLI.