The choice of embedding media affects image quality, tissue R2, and susceptibility behaviors in post‐mortem brain MR microscopy at 7.0T

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 (D2O), (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 D2O. Formalin fixation, and its use as embedding medium for scanning, increased tissue R2*. Imaging with agarose, D2O, 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 D2O embedding. Formalin significantly increased R2* causing noisier data and increased QSM variance.