Fixel-based Analysis of Diffusion MRI: Methods, Applications, Challenges and Opportunities

•The fixel-based analysis framework was proposed for fibre-specific statistical analysis of diffusion MRI data.•A “fixel” represents an individual fibre population in a voxel, allowing for increased specificity over voxel-wise measures.•A state-of-the-art fixel-based analysis pipeline consists of several bespoke steps, but is conceptually similar to a voxel-based analysis.•Fixel-based analysis has seen increased adoption recently, with 75 published studies to date.•The framework has unique benefits and future opportunities, but specific challenges and limitations exist as well. Diffusion MRI has provided the neuroimaging community with a powerful tool to acquire in-vivo data sensitive to microstructural features of white matter, up to 3 orders of magnitude smaller than typical voxel sizes. The key to extracting such valuable information lies in complex modelling techniques, which form the link between the rich diffusion MRI data and various metrics related to the microstructural organization. Over time, increasingly advanced techniques have been developed, up to the point where some diffusion MRI models can now provide access to properties specific to individual fibre populations in each voxel in the presence of multiple “crossing” fibre pathways. While highly valuable, such fibre-specific information poses unique challenges for typical image processing pipelines and statistical analysis. In this work, we review the “Fixel-Based Analysis” (FBA) framework, which implements bespoke solutions to this end. It has recently seen a stark increase in adoption for studies of both typical (healthy) populations as well as a wide range of clinical populations. We describe the main concepts related to Fixel-Based Analyses, as well as the methods and specific steps involved in a state-of-the-art FBA pipeline, with a focus on providing researchers with practical advice on how to interpret results. We also include an overview of the scope of all current FBA studies, categorized across a broad range of neuro-scientific domains, listing key design choices and summarizing their main results and conclusions. Finally, we critically discuss several aspects and challenges involved with the FBA framework, and outline some directions and future opportunities. [Display omitted]