High-field ex vivo brain MRI

All scanning was performed on a 14 T vertical Bruker Micro imaging system with a 30 mm RF coil. The ex vivo brains were rehydrated in phosphate-buffered saline for at least 3 days before imaging and immersed in perfluoro polyether (FOMBLIN^®, Solvay Specialty Polymers Italy SpA) to avoid magnetic susceptibility artifacts during MRI scanning. Diffusion weighted image (DWI) was achieved using a three-dimensional echo planar imaging (EPI) sequence with eight segments: TE/TR = 31/800 ms, b = 3,800 s/mm², 32 gradient directions, δ/Δ = 3/18 ms, 0.16 × 0.16 × 0.16 mm³ voxel size, and two acquisitions at b = 0 s/mm². Here, the b values were chosen to induce similar diffusion signal attenuation as conventional DTI in vivo (b around 1,000 s/mm²) as the diffusivity in ex vivo brain is around 3–4 times smaller than that in in vivo brain. Similar b values were also used by other groups for ex vivo studies (Irfanoglu et al., 2016 (link); Haber et al., 2017 (link)). DWIs with the opposite phase-encoded directions were acquired at b = 0 s/mm² for geometric distortion correction for EPI. The total time for DWI acquisitions was 7 h 20 min 58 s. T₂-weighted images were obtained using a three-dimensional multislice multi-echo sequence (MSME) with the same spatial dimensions as DWIs: TE/TR = 4/1,000 ms and 32 echoes.