Anima: an open-source repository for Empenn research

We are distributing the ITK/VTK C++ implementation of the Empenn team research contributions. It is continuously being updated with new research software. As of now, it contains tools for:

  • image registration: linear and non linear block matching registration, EPI distortion correction
  • statistical analysis (group comparison, patient to group comparison)
  • diffusion imaging (model estimation, tractography, etc.)
  • quantitative MRI processing (quantitative relaxation times estimation, MWF estimation, MR simulation)
  • image denoising (NL-Means) and filtering
  • segmentation tools (Graph cut segmentation and multiple sclerosis lesion segmentation).

In addition, we have also released Anima scripts that use the Anima executables as tools to perform more complex operations, including brain extraction, atlasing, relaxometry or diffusion multi-compartment models estimation.

Anima is available open source and in binary versions. Here are links to the main website and documentation for Anima and Anima scripts:

  • Main website. Includes links to documentation, main github repositories links, downloads, and information on how to contribute or cite Anima and Anima scripts.
  • Documentation website. This documentation contains information on how to clone and compile Anima. It also contains descriptions as well as paper references for each of the algorithms.
  • Binary releases. Up-to-date binary releases are made available from there.

In addition to the documentation, you can subscribe to the users mailing list by subscribing to the anima-users mailing list. If you find a bug in the code, don't hesitate also to submit an issue.