Anima v3.0 release

As part of an ongoing effort to provide our published research code, we have released Anima v3.0 in March 2018. Anima is a set of ITK/VTK based libraries and multi-platform command line tools for medical image analysis. It contains software for image registration (linear and non linear block matching registration, EPI distortion correction), statistical analysis (group comparison, patient to group comparison), diffusion imaging (DTI and multi-compartment model estimation, tractography, etc.), quantitative MRI processing (quantitative relaxation times estimation, myelin water fraction estimation, MR simulation), image denoising and filtering, and segmentation tools (Graph cut segmentation and multiple sclerosis lesion segmentation).

Among new things in v3.0 are the following:

  • New T2 and B1 estimation of mono-component T2 relaxation times from relaxometry sequences
  • New multi-compartment T2 and myelin water fraction estimation tools from relaxometry sequences
  • Update tractography algorithms (probabilistic tractography does not use DWI images anymore, output compatible with medInria 3.0)
  • Add Taquet et al similarity metrics for multi-tensors registration
  • Correct border handling errors in DTI and MCM registration algorithms
  • Add isosurface extraction tool from binary segmentation
  • Correct rare errors in DTI estimation filter
  • Update Eddy current experimental tool to handle well movement correction and distortion (the first one being applied to gradients, not the second one)
  • Other minor bug corrections/evolutions

Anima is available as a Github repository and compiled binaries, including some non open-source tools, for various OSes (OSX, Fedora, Ubuntu, Windows).

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