2015 BRAINSFit registration in SimpleITK

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Case 25
High irregulations in ITKv4
Resolved Irregulations ins ITKv4

Key Investigators

  • Peter Behringer
  • Andriy Fedorov
  • Dženan Zukić

Project Description


  • Our registration module for b-spline deformable registration of prostate MRI uses BRAINSFit in Slicer4/ITKv4.
  • One issue that we are getting with Slicer4/ITKv4 is that they are a lot more irregular and unrealistic than what we used to get in Slicer3/ITKv3 (see summary here)
  • The Slicer4/ITKv4 registration tool should be comparable with the functionality we had in Slicer3/ITKv3, which was evaluated here

Approach, Plan

  • Implement a subset of BRAINSFit functionality used for supporting in-bore MRI-guided prostate biopsy in SimpleITK
  • Get ideas from the community how the irregularity can be avoided and implemented in SimpleITK


  • Initialization and rigid registration is implemented using SimpleITK
  • We tracked the issue down using various parameters
  • We used strongly dilated masks for the BSpline registration and results are looking much better