# Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI : Part 3—Ex vivo imaging: Data processing, comparisons with microscopy, and tractography

Kurt G. Schilling, Amy F. D. Howard, Francesco Grussu, Andrada Ianus, Brian Hansen, Rachel L. C. Barrett, Manisha Aggarwal, Stijn Michielse, Fatima Nasrallah, Warda Syeda, Nian Wang, Jelle Veraart, Alard Roebroeck, Andrew F. Bagdasarian, Cornelius Eichner, Farshid Sepehrband, Jan Zimmermann, Lucas Soustelle, Christien Bowman, Benjamin C. Tendler, Andreea Hertanu, Ben Jeurissen, Marleen Verhoye, Lucio Frydman, Yohan van de Looij, David Hike, Jeff F. Dunn, Karla Miller, Bennett A. Landman, Noam Shemesh, Adam Anderson, Emilie McKinnon, Shawna Farquharson, Flavio Dell'Acqua, Carlo Pierpaoli, Ivana Drobnjak, Alexander Leemans, Kevin D. Harkins, Maxime Descoteaux, Duan Xu, Hao Huang, Mathieu D. Santin, Samuel C. Grant, Andre Obenaus, Gene S. Kim, Dan Wu, Denis Le Bihan, Stephen J. Blackband, Luisa Ciobanu, Els Fieremans, Ruiliang Bai, Trygve B. Leergaard, Jiangyang Zhang, Tim B. Dyrby, G. Allan Johnson, Julien Cohen-Adad, Matthew D. Budde, Ileana O. Jelescu

Magnetic Resonance in Medicine · 2025 · Review

https://doi.org/10.1002/mrm.30424

## Summary

The third ISMRM preclinical diffusion MRI paper addresses ex vivo image processing, comparisons with microscopy, and tractography. It explains how fixed-tissue experiments require choices that differ from in vivo workflows. Community recommendations and unresolved questions guide the design and interpretation of rigorous, reproducible validation studies.

## Study overview

Ex vivo diffusion MRI offers detailed images and opportunities for direct comparison with microscopy, but those advantages introduce distinct processing and interpretation challenges. The final paper in this three-part series covers preprocessing, diffusion modeling, microscopy comparisons, and tractography using ex vivo specimens. It discusses how experimental conditions and tissue preparation influence the resulting measurements and what is needed to connect MRI features to histological evidence. The authors present practical recommendations while identifying areas where firm guidance remains unavailable. The paper supports reproducible validation work and complements the acquisition-focused recommendations in Part 2 of the series.

## Findings / topics

- Addresses preprocessing and modeling choices specific to ex vivo tissue.
- Discusses comparisons with microscopy and tractography validation.
- Highlights gaps where methodological evidence does not yet support firm guidance.

## Resources

- [Original work](https://onlinelibrary.wiley.com/doi/10.1002/mrm.30424)
- [Open full text](https://pmc.ncbi.nlm.nih.gov/articles/PMC11971500/)

Lab page: https://www.microstructure-connectivity-lab.com/publications/preclinical-dmri-part-3/

This is a research summary, not the full article.