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Software Open Access

SimpleElastix: v0.9.1

Bradley Lowekamp; gabehart; Daniel Blezek; Kasper Marstal; Luis Ibanez; Dave Chen; Matt McCormick; Dan Mueller; Hans Johnson; David Cole; Ziv Yaniv; Jorrit Posthuma; Richard Beare; Ali Ghayoor; Arnaud Gelas; ltong1130ztr; adizhol; Jean-Christophe Fillion-Robin; Anthony; Brad King; David Doria


  • Completely rewritten core. Internally, images are now registered using the ITK-style ElastixFilter and TransformixFilter library interfaces developed specifically for SimpleElastix. This brings SimpleElastix on par with the original elastix command line interface by adding:
    • Support for multiple fixed images, multiple moving images, multiple fixed masks and multiple moving masks
    • Support for point set registration and warping of point sets with SimpleTransformix
    • Support for writing the spatial jacobian, deformation field and determinant of the spatial jacobian to disk,
    • Support for initial transforms
  • Completely rewritten test suite covering a larger number of registration algorithms performing more thorough unit testing
  • Add method ExecuteInverse() for automatically obtaining the inverse transformation even for methods without an analytical inverse
  • Add valgrind memcheck utility script
  • Add groupwise affine registration method
  • Add two new groupwise similarity metrics
  • Default parameter maps are now added automatically when SimpleElastix class is instantiated. This means the user does not have to supply a parameter map before starting registration but a simple Elastix(fixedImage, movingImage) call is enough.
  • Add support for 4D images to JoinSeriesImageFilter
  • Add preconfigured SplineKernel parameter map
  • Add checks and better diagnostic messages for many typical errors
  • Fixed an issue that prevented transformix from transforming 4D images
  • Add support for all pixel types by default
  • Compile in Release mode by default
  • SimpleITK.ParameterMapList() changed name to VectorOfParameterMap() to align with SimpleITK naming.
  • SimpleTransformix.SetInputImage() changed name to SimpleTransformix.SetMovingImage() to align with the SimpleElastix.SetMovingImage() method and convey its role more clearly.
  • PrettyPrint() changed name to PrintParameterMap()
  • Updated and improved default parameter maps.
  • Switched to a Github elastix mirror in favor of official elastix SVN reposity due to stability problems.

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