Additional tools

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

Contributions of users are very much welcomed!

Contents

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).

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, Octave, C#, and Lua.

3D Slicer extension

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

Matlab interfaces

Toolbox by Pedro A. Valdes Hernandez

A set of Matlab functions to call elastix, read, edit and write parameter files, etc. Click here for wiki page

ElastixFromMatlab toolbox

https://sourcesup.renater.fr/elxfrommatlab/

ElastixToolbox at project Gerardus

ElastixToolbox at project Gerardus: Read/write parameter files, Matlab interfaces to elastix and transformix, 2D grayscale/colour images, concatenation of transforms.

MelastiX by Rob Campbell

MelastiX at the File Exchange (FEX page also contains GitHub link): Call Elastix directly on MATLAB matrices from within MATLAB. Facility for performing inverse transforms, concatenation of transforms, YML preferences file. Examples.


MeVisLab interface

A set of MeVisLab modules have been created for configuration and execution of elastix and transformix from within MeVisLab , see MeVisLab interface wiki.

Contributed by Marijn van Stralen, Image Sciences Institute, UMC Utrecht, the Netherlands.

Atlas generation example

This example shows how to generate an atlas using non-rigid registation 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.

statismo-elastix

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

Add your own tools here!

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