High-resolution post-mortem anatomical ultra-high field MRI of the macaque brain (v1)

A female macaque (Macaca fascicularis) brain specimen was scanned ex vivo using a preclinical ultra-high field (UHF) magnetic resonance imaging (MRI) system at 11.7T to obtain a mesoscopic anatomical MRI dataset. 100 µm and 180 µm isotropic resolution images were acquired using T2-weighted sequences.
A dedicated preprocessing pipeline was developed to perform various file conversions (Bruker native format, DICOM format, NIfTI format), to correct images from signal bias using an N4BiasFieldCorrection algorithm and to compute diffeomorphic transformations from the native space to the MEBRAINS template space. The same diffeomorphic transformation was used to resample both 180 µm and 100 µm datasets in the MEBRAINS template using the MEBRAINS T2 contrast, with an additional linear transformation applied between the 100 µm and the 180 µm datasets, to produce two datasets including :
– a high resolution 100 µm anatomical UHF MRI dataset,
– a high resolution 180 µm anatomical UHF MRI dataset.
These two datasets will enable the further processing of a 3D map of segmented cortical and deep gray structures at the mesoscopic scale.