May 11, 2016 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

New

• 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.