An interactive registration tool that manages viewing and manipulating of sets of fiducials
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An interactive registration tool that manages viewing and manipulating of sets of fiducials

This is a work-in-progress that will ultimately be an extension or core module of 3D Slicer.

Some background information is here:


To test: You need to checkout two repositories (1) this one and (2)

If you checked them out to /tmp, then you can start slicer as follows:


./Slicer --additional-module-paths /tmp/CompareVolumes /tmp/LandmarkRegistration

(on windows you run "Slicer.exe " from a console. On mac, you use "open ")


As of Nov 5, 2013 the master has been converted to use Markups rather than Annotations, meaning that it works with Slicer 4.3.1 and later. Older versions of Slicer are / will not be supported.



  • load the two volumes to register
  • enter the LandmarkRegistration module
  • select Fixed and Moving (do not select transformed)
  • scroll to the Registration area and select Linear
  • enable the Registration Active checkbox (this will create a transformed volume)
  • pick Axi/Sag/Cor in the Visualization box (this will create a custom layout with fixed on top, moving in the middle, and fixed + transformed on the bottom)
  • place a fiducial on either the fixed or moving volumes (a corresponding one will be created on the other volume)
  • drag the fiducials in the fixed and moving volumes until they are on the same anatomical location. The blended view will update automatically on mouse release.
  • place and adjust fiducials until registration is good.
  • Option: Similarity mode is Rigid + Scale and can be good for some cross-subject registration


  • Affine mode requires more landmarks but should work
  • Thin-Plate spline mode works but does not automatically update (click Apply to calculate). It overwrites the transformed volume so you can't go back to Linear mode from Thin-Plate mode).
  • Hybrid B-Spline mode is still under development.