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

Abstract

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. 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. 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. 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.