Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2—Ex vivo imaging: Added value and acquisition

Abstract

Diffusion MRI; Diffusion tensor; Ex vivo

Resonancia magnética de difusión; Tensor de difusión; Ex vivo

Ressonància magnètica de difusió; Tensor de difusió; Ex vivo

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher SNR and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts for improved microstructure and connectivity characterization. Another major advantage of ex vivo dMRI is the direct comparison with histological data, as a crucial methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents “Part 2” of a three-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We first give general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

The authors acknowledge financial support from: the National Institutes of Health (K01EB032898, R01AG057991, R01NS125020, R01EB017230, R01EB 019980, R01EB031954, R01CA160620, R01NS109090), the National Institute of Biomedical Imaging and Bioengineering (R01EB031765, R56EB031765), the National Institute on Drug Abuse (P30DA048742), the Secretary of Universities and Research (Government of Catalonia) Beatriu de Pinós postdoctoral fellowship (2020 BP 00117), “la Caixa” Foundation Junior Leader fellowship (LCF/BQ/PR22/11920010), the Research Foundation Flanders (FWO: 12M3119N), the Belgian Science Policy Prodex (Grant ISLRA 2009–1062), the μNEURO Research Center of Excellence of the University of Antwerp, the Institutional research chair in Neuroinformatics (Sherbrooke, Canada), the NSERC Discovery Grant, the European Research Council Consolidator grant (101044180), the Canada Research Chair in Quantitative Magnetic Resonance Imaging [950-230815], the Canadian Institute of Health Research [CIHR FDN-143263], the Canada Foundation for Innovation [32 454, 34 824], the Fonds de Recherche du Québec—Santé [322736], the Natural Sciences and Engineering Research Council of Canada [RGPIN-2019-07244], the Canada First Research Excellence Fund (IVADO and TransMedTech), the Courtois NeuroMod project, the Quebec BioImaging Network [5886, 35 450], the Mila—Tech Transfer Funding Program and the Swiss National Science Foundation (Eccellenza Fellowship PCEFP2_194260), the Wellcome Trust (202788/Z/16/A, 203139/Z/16/Z and 203139/A/16/Z).