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Dmipy, A Diffusion Microstructure Imaging Toolbox in Python to Improve Research Reproducibility

  • Abib AlimiEmail author
  • Rutger Fick
  • Demian Wassermann
  • Rachid Deriche
Conference paper
Part of the Mathematics and Visualization book series (MATHVISUAL)

Abstract

Non-invasive estimation of brain white matter microstructure features using diffusion MRI—otherwise known as Microstructure Imaging—has become an increasingly diverse and complicated field over the last decade. Multi-compartment-based models have been a popular approach to estimate these features. In this work, we present Diffusion Microstructure Imaging in Python (Dmipy), a diffusion MRI toolbox which allows accessing any multi-compartment-based model and robustly estimates these important features from single-shell, multi-shell, and multi-diffusion time, and multi-TE data. Dmipy follows a building block-based philosophy to microstructure imaging, meaning a multi-compartment model can be constructed and fitted to dMRI data using any combination of underlying tissue models, axon dispersion-or diameter distributions, and optimization algorithms using less than 10 lines of code, thus helps improve research reproducibility. In describing the toolbox, we show how Dmipy enables to easily design microstructure models and offers to the users the freedom to choose among different optimization strategies. We finally present three advanced examples of highly complex modeling approaches which are made easy using Dmipy.

Keywords

Diffusion MRI Microstructure imaging dMRI Multi-compartment models Python Free open source software 

Notes

Acknowledgements

This work was partly supported by ANR “MOSIFAH” under ANR-13-MONU-0009-01, the ERC under the European Union’s Horizon 2020 research and innovation program (ERC Advanced Grant agreement No 694665:CoBCoM).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Abib Alimi
    • 1
    Email author
  • Rutger Fick
    • 2
  • Demian Wassermann
    • 3
  • Rachid Deriche
    • 1
  1. 1.Athena, Inria, Université Côte d’AzurSophia AntipolisFrance
  2. 2.TheraPanaceaParisFrance
  3. 3.Parietal, Inria, CEA, Université Paris-SaclayParisFrance

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