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The value of preclinical diffusion MRI (dMRI) is substantial. While dMRIenables in vivo non-invasive characterization of tissue, ex vivo dMRI isincreasingly used to probe tissue microstructure and brain connectivity. Exvivo dMRI has several experimental advantages including higher signal-to-noiseratio and spatial resolution compared to in vivo studies, and enabling moreadvanced diffusion contrasts. Another major advantage of ex vivo dMRI is thedirect comparison with histological data as a methodological validation.However, there are a number of considerations that must be made when performingex vivo experiments. The steps from tissue preparation, image acquisition andprocessing, and interpretation of results are complex, with decisions that notonly differ dramatically from in vivo imaging of small animals, but ultimatelyaffect what questions can be answered using the data. This work represents"Part 2" of a 3-part series of recommendations and considerations forpreclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with afocus on the value that ex vivo imaging adds to the field of dMRI andconsiderations in ex vivo image acquisition. We give general considerations andfoundational knowledge that must be considered when designing experiments. Wedescribe differences in specimens and models and discuss why some may be moreor less appropriate for different studies. We then give guidelines for ex vivoprotocols, including tissue fixation, sample preparation, and MR scanning. Ineach section, we attempt to provide guidelines and recommendations, but alsohighlight areas for which no guidelines exist (and why), and where future workshould lie. An overarching goal herein is to enhance the rigor andreproducibility of ex vivo dMRI acquisitions and analyses, and thereby advancebiomedical knowledge.

Considerations and recommendations from the ISMRM Diffusion Study Group  for preclinical diffusion MRI: Part 2 -- Ex vivo imaging: added value and  acquisition