A Reproducible Diffusion MRI Processing Pipeline for Microstructure and Glymphatic Analysis Using Neurodesk Containers v1

Résumé

This protocol describes an accessible and reproducible end-to-end pipeline for diffusion MRI processing and microstructure analysis using containerized tools within the Neurodesk environment on Google Colab. It enables standardized diffusion MRI preprocessing, microstructural reconstruction, white matter hyperintensity segmentation, and glymphatic assessment through BIDS-compliant workflows designed for clinical and research diffusion MRI data, including 1.5 T acquisitions. Successful execution yields organized derivatives including image quality metrics, anatomically preprocessed structural data, preprocessed diffusion datasets, microstructural reconstructions such as fiber orientation distributions or tensor-based measures, and white matter hyperintensity masks. The pipeline also produces diffusivity components and ALPS index outputs that support quantitative assessment of white matter microstructure and perivascular diffusion characteristics in a reproducible analysis framework.

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