MRI Brain Imaging in Fluorinert Liquid

To remove background field effects and to keep the brain moist, formalin- fixed brains were placed in a plastic container filled with 3M fluorinert electronic liquid (FC-770, Parallax Technology, Inc.), which had the similar susceptibility as the brain^{40 (link)}. The brains were rocked gently in room temperature for 12–24 h to allow air bubbles to escape^{40 (link)–42 (link)}. MRI scans were acquired at a 3T Siemens Trio MRI scanner with a 32-channel head coil (Siemens Medical Solutions) using 3D multi-echo gradient recalled echo (GRE) and 3D T2-weighted turbo spin echo sequences. For the initial 5 brains, multi-echo GRE scans were acquired in 112 slices of 0.5 mm thickness (no gap), with field of view = 224 mm², matrix size = 448 × 448, repetition time = 50 ms, echo time (TE)₁/spacing/TE₉ = 5/5/45 ms, flip angle = 20°, number of excitations = 4. The initial 5 T2 scans were acquired in 224 slices of 0.5 mm thickness (no gap), with field of view = 256 mm², matrix size = 512 × 512, repetition time = 3,200 ms, TE = 371 ms, Turbo factor = 269, number of excitations = 2. To minimize susceptibility artifacts caused by residual water/air bubbles, the subsequent 12 multi-echo GRE scans were acquired in 240 slices of 0.6 mm thickness (no gap), with field of view = 224 mm², matrix size = 384 × 384, repetition time = 30 ms, TE₁/spacing/TE₆ = 2.25/2.25/13.50 ms, flip angle = 20°, number of excitations = 4. The subsequent 12 T2 scans were acquired in 288 slices of 0.5 mm thickness (no gap), with field of view = 256 mm², matrix size = 512 × 512, repetition time = 3,200 ms, TE = 371 ms, Turbo factor = 269, number of excitations = 3.