Whole-brain ex vivo MRI has proven extremely valuable in neuroscience research, but detailed descriptions of the specific preparation and packaging steps to minimize motion, susceptibility artifacts, and background signal are often missing from reports of experimental findings. We present the design of a reproducible container and a detailed protocol that yield whole-brain images uncorrupted by susceptibility artifacts. The most important steps to eliminate susceptibility artifacts due to residual air bubbles are removal of the leptomeninges, application of vacuum to dislodge bubbles, immersion in Fluorinert, and rolling of the sealed container, although removal of leptomeninges may be undesirable in some cases.
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