Faculty Collaboration Database

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small-animal imaging. Magn Reson Med 2025 Jun;93(6):2507-2534

Date

02/26/2025

Pubmed ID

40008568

Pubmed Central ID

PMC11971505

DOI

10.1002/mrm.30429

Scopus ID

2-s2.0-105002179184 (requires institutional sign-in at Scopus site)   10 Citations

Abstract

Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the resultant data. This work aims to present selected considerations and recommendations from the diffusion community on best practices for preclinical dMRI of in vivo animals. We describe the general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss why some may be more or less appropriate for different studies. We, then, give recommendations for in vivo acquisition protocols, including decisions on hardware, animal preparation, and imaging sequences, followed by advice for data processing including preprocessing, model-fitting, and tractography. Finally, we provide an online resource that lists publicly available preclinical dMRI datasets and software packages to promote responsible and reproducible research. In each section, we attempt to provide guides and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should focus. Although we mainly cover the central nervous system (on which most preclinical dMRI studies are focused), we also provide, where possible and applicable, recommendations for other organs of interest. An overarching goal is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

Author List

Jelescu IO, Grussu F, Ianus A, Hansen B, Barrett RLC, Aggarwal M, Michielse S, Nasrallah F, Syeda W, Wang N, Veraart J, Roebroeck A, Bagdasarian AF, Eichner C, Sepehrband F, Zimmermann J, Soustelle L, Bowman C, Tendler BC, Hertanu A, Jeurissen B, Verhoye M, Frydman L, van de Looij Y, Hike D, Dunn JF, Miller K, Landman BA, Shemesh N, Anderson A, McKinnon E, Farquharson S, Dell'Acqua F, Pierpaoli C, Drobnjak I, Leemans A, Harkins KD, Descoteaux M, Xu D, Huang H, Santin MD, Grant SC, Obenaus A, Kim GS, Wu D, Le Bihan D, Blackband SJ, Ciobanu L, Fieremans E, Bai R, Leergaard TB, Zhang J, Dyrby TB, Johnson GA, Cohen-Adad J, Budde MD, Schilling KG

Author

Matthew Budde PhD Associate Professor in the Neurosurgery department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Brain
Diffusion Magnetic Resonance Imaging
Image Processing, Computer-Assisted
Mice
Reproducibility of Results
Software