High-Field MRI of Fixed Brain Samples

The fixed brains were rinsed in PBS and placed into a custom-built MRI-compatible tube filled with Fluorinert (Sigma-Aldrich, Inc. St. Louis, Mo.). MRI was performed on a 9.4 T horizontal bore magnet (Bruker, Billerica, Mass.) with custom-made ¹H radiofrequency coils (14 mm diameter)^{14 (link)}. Coronal slices of 800 μm thickness were acquired for both anatomical and DTI images. Anatomical images were acquired using a spin-echo sequence with repetition time (TR) of 3,000 ms and an echo time (TE) of 10 ms, with a maximum of 16 averages with an in-plane resolution of 100 μm × 100 μm. DTI acquisition followed the Sjekta-Tanner spin-echo diffusion-weighted sequence with a diffusion gradient δ=5 ms and a delay Δ=15 ms between diffusion gradients^{15 (link)}. TR was 2,000 ms and TE was 25.1 ms. Two Shinnar-Le Roux (SLR) pulses of 1 ms each were used for excitation and inversion. Data for each slice were acquired with a 12×64 matrix and then zero-filled to 256×256. A total of 16 different non-collinear diffusion weighted directions were acquired with the same b=1,000 s/mm². Previous studies comparing fixed vs. in-vivo DTI have shown no significant differences in DTI parameters^{16 (link)–18 (link)}.