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To investigate this, our study evaluated the impact of 5 widely used media on: (1) image quality, (2) contrast of high spatial resolution gradient\u2010echo (T<jats:sub>1<\/jats:sub> and T<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup>\u2010weighted) MR images, (3) effective transverse relaxation rate (R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup>), and (4) quantitative susceptibility measurements (QSM) of post\u2010mortem brain specimens.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Five formaldehyde\u2010fixed brain slices were scanned using 7.0T MRI in: (1) formaldehyde solution (formalin), (2) phosphate\u2010buffered saline (PBS), (3) deuterium oxide (D<jats:sub>2<\/jats:sub>O), (4) perfluoropolyether (Galden), and (5) agarose gel. SNR and contrast\u2010to\u2010noise ratii (SNR\/CNR) were calculated for cortex\/white matter (WM) and basal ganglia\/WM regions. In addition, median R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup> and QSM values were extracted from caudate nucleus, putamen, globus pallidus, WM, and cortical regions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>PBS, Galden, and agarose returned higher SNR\/CNR compared to formalin and D<jats:sub>2<\/jats:sub>O. Formalin fixation, and its use as embedding medium for scanning, increased tissue R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup>. Imaging with agarose, D<jats:sub>2<\/jats:sub>O, and Galden returned lower R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup> values than PBS (and formalin). No major QSM offsets were observed, although spatial variance was increased (with respect to R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup> behaviors) for formalin and agarose.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Embedding media affect gradient\u2010echo image quality, R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup>, and QSM in differing ways. In this study, PBS embedding was identified as the most stable experimental setup, although by a small margin. Agarose and Galden were preferred to formalin or D<jats:sub>2<\/jats:sub>O embedding. Formalin significantly increased R<jats:sub>2<\/jats:sub><jats:sup>*<\/jats:sup> causing noisier data and increased QSM variance.<\/jats:p><\/jats:sec>","DOI":"10.1002\/mrm.27595","type":"journal-article","created":{"date-parts":[[2018,12,3]],"date-time":"2018-12-03T05:19:23Z","timestamp":1543814363000},"page":"2688-2701","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["The choice of embedding media affects image quality, tissue R<sub>2<\/sub><sup>*<\/sup>, and susceptibility behaviors in post\u2010mortem brain MR microscopy at 7.0T"],"prefix":"10.1002","volume":"81","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4877-9642","authenticated-orcid":false,"given":"Petr","family":"Dusek","sequence":"first","affiliation":[{"name":"Department of Neurology Charles University, 1st Faculty of Medicine and General University Hospital in Prague Praha Czech Republic"},{"name":"Department of Radiology Charles University, 1st 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