Additional tools

This page contains links to useful tools/scripts that provide additional functionality on top of elastix.

Contributions of users are very much welcomed!

1. ITKTools
   https://github.com/ITKTools https://github.com/ITKTools
   A collection of general purpose image processing programs, based on ITK. Includes a program to compute overlap between segmentations (which is often used to evaluate image registrations).

2. SimpleElastix
   http://simpleelastix.github.io/
   SimpleElastix is an extension of SimpleITK that offers user-friendly access to the popular image registration algorithms of the elastix C++ library. This makes state-of-the-art medical image registration really easy to do in languages like C++, Python, Java, R, Ruby, C# and Lua.

3. 3DSlicer extension
   Thanks to Andras Lasso, elastix is now available as a plug-in for 3DSlicer. If you download and install 3DSlicer then you can install the elastix extension from Slicer's extension manager by a few clicks.

4. Matlab interfaces

• ElastixFromMatlab toolbox
  https://sourcesup.renater.fr/elxfrommatlab/

• ElastixToolbox at project Gerardus
  https://github.com/rcasero/gerardus/tree/master/matlab/ElastixToolbox
  Read/write parameter files, Matlab interfaces to elastix and transformix, 2D grayscale/colour images, concatenation of transforms.

• MelastiX by Rob Campbell
  http://www.mathworks.com/matlabcentral/fileexchange/52982-melastix
  MelastiX at the Matlab File Exchange, which also contains a GitHub link: Call elastix directly on MATLAB matrices from within MATLAB. Facility for performing inverse transforms, concatenation of transforms, YML preferences file, examples.

5. MeVisLab interface
   https://github.com/MeVisLab/communitymodules
   A set of MeVisLab modules have been created for configuration and execution of elastix and transformix from within MeVisLab, see the MeVisLab interface wiki.
   Contributed by Marijn van Stralen, Image Sciences Institute, UMC Utrecht, the Netherlands.

6. Atlas generation example
   This example shows how to generate an atlas using non-rigid registration in elastix, based on artificial population data.
   The parameter files, python scripts, and data can be found on the atlas generation example wiki page.
   Contributed by Roy van Pelt, Biomedical Image Analysis group, Eindhoven University of Technology, the Netherlands.

7. statismo-elastix
   https://github.com/statismo/statismo-elastix
   A small elastix user component that provides an interface to statismo, an open source library for statistical shape modeling.
   This allows to perform statistically constrained registration and atlas-based segmentation in elastix.

8. itk-elastix https://github.com/InsightSoftwareConsortium/ITKElastix Provides an ITK Python interface to elastix, including binary Python packages pip install itk-elastix, registered_image = itk.elastix_registration_method(fixed_image, moving_image).

=== Add your own tools here! ===