We used magnetic resonance imaging to study the anatomy of cortical regions, nuclear groups and major forebrain tracts in the brains of three peramelemorphian marsupials (Perameles nasuta, Isoodon obesulus, Macrotis lagotis). These brains had been stored in formaldehyde solution in a museum collection for more than 80 years, and one of our goals was to demonstrate the feasibilty of extracting detailed comparative neuroanatomical information from the preserved brains of rare, endangered and extinct animals. High resolution anatomical and Diffusion Tensor Imaging was performed using a 9.4-T Bruker BioSpec 94/20 Avance III MRI system (Bruker, Ettlingen, Germany) located at the Biological Resources Imaging Laboratory at the University of New South Wales in Sydney. For image aquisition the system was equipped with gradients of 660 mT m-1 maximum strength and 4570 Tm s-1 slew rate (BGA-12S HP, Bruker, Ettlingen, Germany) and a 50 mm Quadrature Receive/Transmit RF-coil (RAPID Biomedical, Wuerzburg, Germany) for signal generation and reconstruction. We were able to differentiate areal and laminar topography within isocortical areas (primary somatosensory – S1; and visual - V1, V2), as well as subdivisions within olfactory and limbic allocortical regions (cingulate, hippocampal). Resolution of subcortical structures was sufficient to differentiate a and b segments within the visual nucleus of the thalamus. We identified several previously unrecognised longitudinal association fibre systems as well as a rich array of sensory thalamocortical connections. Our findings demonstrate the feasibility of using this sort of imaging of archived brains to analyze the neuranatomy of rare and evolutionarily significant species.