MouseFlow: a pipeline for mouse brain diffusion MRI data, generating tractograms and diffusion metrics with quality controls

Motivation: Diffusion MRI in rodents has significant potential to enhance our understanding of brain networks. Goal(s): MouseFlow provides a fully automated diffusion image processing pipeline for the mouse brain that enhances reproducibility and quality of processing and analysis, addressing a crucial need in the field. Approach: This pipeline generates diffusion metrics, tractograms, and incorporates quality control measures to promote reproducibility. Results: We tested the pipeline under varying parameters, including sequence, field strength, pathologies, and resolution. MouseFlow supports reproducible practices, fostering progress in translational neuroscience research. Impact: MouseFlow enables researchers studying the rodent brain to standardise diffusion MRI workflows, improving reproducibility and comparability between studies. It facilitates studying brain connectivity in healthy and pathological conditions, advancing translational neuroscience with more robust and reliable data.