Ex vivo diffusion MRI protocol optimization on the Connectome 2.0 scanner for reconstructing cortico-subcortical projections

Motivation: As part of the BRAIN Initiative Connectivity across Scales (CONNECTS) program, we are planning to image ex vivo human brains with mesoscopic diffusion MRI (dMRI) and downstream correlative microscopy. Goal(s): The goal of this study is to optimize the dMRI protocol, with an emphasis on reconstructing pathways relevant to deep-brain stimulation. Approach: We perform the first study evaluating ex vivo dMRI protocols on the Connectome 2.0 scanner, by comparing dMRI tractography against reference tracts from an atlas annotated by neuroanatomic experts. Results: Our preliminary evaluation suggests a protocol for satisfactory reconstruction of the tracts of interest at 0.55mm resolution. Impact: We seek to establish a cutting-edge diffusion MRI protocol to collect data on ex vivo human brains, which will be accompanied by correlative microscopy and serve as a resource for the research community, to benefit both methodological and neuroanatomic studies.