  The value of in vivo preclinical diffusion MRI (dMRI) is substantial.
Small-animal dMRI has been used for methodological development and validation,
characterizing the biological basis of diffusion phenomena, and comparative
anatomy. Many of the influential works in this field were first performed in
small animals or ex vivo samples. 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 data. This
work aims to serve as a reference, presenting selected recommendations and
guidelines from the diffusion community, on best practices for preclinical dMRI
of in vivo animals. In each section, we also highlight areas for which no
guidelines exist (and why), and where future work should focus. We first
describe the value that small animal imaging adds to the field of dMRI,
followed by general considerations and foundational knowledge that must be
considered when designing experiments. We briefly describe differences in
animal species and disease models and discuss how they are appropriate for
different studies. We then give guidelines for in vivo acquisition protocols,
including decisions on hardware, animal preparation, imaging sequences and data
processing, including pre-processing, model-fitting, and tractography. Finally,
we provide an online resource which lists publicly available preclinical dMRI
datasets and software packages, to promote responsible and reproducible
research. An overarching goal herein is to enhance the rigor and
reproducibility of small animal dMRI acquisitions and analyses, and thereby
advance biomedical knowledge.
