Anima v4.0 and Anima scripts v3.0 released

As part of an ongoing effort to provide our published research code, we are happy to release Anima v4.0 and Anima scripts v3.0. Both now have a common website and documentation, where install instructions and binaries downloads for all major OSes are available.

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 Anima v4.0 are the following:

  • use latest versions of ITK (5.1.1) and VTK (9.0.1)
  • switch all tools to double precision (storage and processing)
  • much faster estimation algorithms for multi-compartment relaxometry (animaGammaMixtureT2RelaxometryEstimation and animaGMMT2RelaxometryEstimation)
  • faster distortion correction tools (animaBMDistortionCorrection and animaEddyCurrentCorrection)
  • faster bounded levenberg marquardt optimization for MCM
  • add MCM scalar maps tool
  • MCM file format change for easier use
  • tractography algorithms do not output scalar values along fibers by default, for faster processing and lighter weight output files
  • add fibers counter tool from tractography files
  • faster MCM registration
  • MCM resampling update: sticks and zeppelins can now be interpolated and registered
  • add animaFuzzyDiceMeasure tool for evaluation using generalized Dice
  • add b-value shell selection to ODF estimation
  • fixes in reorientation algorithms for diffusion images registration and resampling
  • under the hood work in registration: resampling now automatically sets default background value to -1024 for CT images
  • bug corrections in NODDI compartment implementation
  • bug corrections in noise generation tool
  • Other minor bug corrections

Among new things in Anima scripts v3.0 are the following:

  • Atlasing scripts now produce all their main results in a residualDir folder and better support input file extensions
  • Updated atlas for brain extraction in additional data
  • Minor bug corrections in diffusion and relaxometry scripts


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