Vnmrj acquisition software v2

All magnetic resonance imaging (MRI) was performed on a 7.0 T horizontal small bore magnet (Varian, Palo Alto, CA, USA) with a custom built 39 mm diameter head quadrature RF coil (David Herlihy, Imperial College London) linked to a Linux-based control console running VnmrJ acquisition software (v2.3, Varian, Palo Alto CA, USA). All acquisitions were performed at room temperature (21°C) on post-mortem samples with brains retained within the skull to avoid artifacts due to dissection or motion, as well as to avoid a tissue-air interface, which could affect cortical measurements. Prior to scanning, skulls were immersed in Fluorinert (Sigma) to provide a hydrogen-free background signal. Ex vivo scanning enables long scanning times that result in high spatial resolution images, which reduce potential confounding imaging artifacts, such as partial volume effects or head motion.

Brains were prepared for ex vivo MR imaging as previously described
(Vernon et al.2011 (link), 2014 (link)) (see also Supplementary materials and methods). Briefly, MR image
acquisition was performed using a 7 T horizontal small bore magnet (Varian, USA) with
custom-made quadrature volume radiofrequency (RF) coil (43 mm inner diameter, Rapid
Biomedical GmbH, Germany) connected to a console running VnmrJ acquisition software (v.
2.3; Varian). A modified multiecho, multislice spin-echo pulse sequence was used for image
acquisition, with the following parameters: field of view = 35 × 35 mm²;
matrix = 192 × 192; repetition time = 4200 ms; echo time = 10, 20, 30, 40, 50, 60, 70,
80 ms; 8 averages, 50 slices, 0.5 mm thick, with a total duration of 2 h 30 min and an in
plane resolution of 187 μm.