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Abstract #0842

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

Elise Cosenza1, Arnaud Boré2, Alex Valcourt Caron2, Valéry Ozenne3, Aurélien Trotier3, Maxime Descoteaux2,4, Sylvain Miraux3,4,5, and Laurent Petit1,4
1Groupe d’Imagerie Neurofonctionnelle – Institut des Maladies Neurodégénératives (GIN-IMN), UMR5293 CNRS, Université de Bordeaux, Bordeaux, France, 2Sherbrooke Connectivity Imaging Laboratory Computer Science Department, Université de Sherbrooke,, Sherbrooke, QC, Canada, 3Centre de Résonance Magnétiques des Systèmes Biologiques (CRMSB), UMR5536 CNRS, Université de Bordeaux, Bordeaux, France, 4International Research Project OpTeam, Bordeaux-Sherbrooke, QC, France, 5Plateforme d’Imagerie Biomédicale (pIBIO), UAR3767 CNRS, Université de Bordeaux, Bordeaux, France

Synopsis

Keywords: Preclinical Image Analysis, Ex-Vivo Applications

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.

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