PURPOSE: The quality and precision of post-mortem MRI microscopy may vary depending on the embedding medium used. To investigate this, our study evaluated the impact of 5 widely used media on: (1) image quality, (2) contrast of high spatial resolution gradient-echo (T1 and T2* -weighted) MR images, (3) effective transverse relaxation rate (R2* ), and (4) quantitative susceptibility measurements (QSM) of post-mortem brain specimens. METHODS: Five formaldehyde-fixed brain slices were scanned using 7.0T MRI in: (1) formaldehyde solution (formalin), (2) phosphate-buffered saline (PBS), (3) deuterium oxide (D2 O), (4) perfluoropolyether (Galden), and (5) agarose gel. SNR and contrast-to-noise ratii (SNR/CNR) were calculated for cortex/white matter (WM) and basal ganglia/WM regions. In addition, median R2* and QSM values were extracted from caudate nucleus, putamen, globus pallidus, WM, and cortical regions. RESULTS: PBS, Galden, and agarose returned higher SNR/CNR compared to formalin and D2 O. Formalin fixation, and its use as embedding medium for scanning, increased tissue R2* . Imaging with agarose, D2 O, and Galden returned lower R2* values than PBS (and formalin). No major QSM offsets were observed, although spatial variance was increased (with respect to R2* behaviors) for formalin and agarose. CONCLUSIONS: Embedding media affect gradient-echo image quality, R2* , 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 D2 O embedding. Formalin significantly increased R2* causing noisier data and increased QSM variance.

Berlin Ultrahigh Field Facility Berlin Germany

Department of Neurology and Center for Stroke Research Berlin Berlin Germany

Department of Neurology and Center for Stroke Research Berlin Charité Universitaetsmedizin Berlin Germany

Department of Neurology Charles University 1st Faculty of Medicine and General University Hospital Prague Praha Czech Republic Department of Radiology Charles University 1st Faculty of Medicine and General University Hospital Prague Praha Czech Republic

Department of Pathology and Molecular Medicine Thomayer Hospital Praha Czech Republic Department of Pathology Charles University 1st Faculty of Medicine and General University Hospital Prague Praha Czech Republic

Institute of Neuropathology University Medicine Göttingen Göttingen Germany

NeuroCure Clinical Research Center Charité Universitaetsmedizin Berlin Germany Medical Imaging Analysis Center AG Basel Switzerland Department of Biomedical Engineering University Basel Switzerland

Wellcome Centre for Human Neuroimaging UCL Institute of Neurology University College London London United Kingdom German Center for Neurodegenerative Diseases Magdeburg Germany

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