Motivation: Loss of neuromelanin (NM) in brainstem structures is evident in pathology in early neurodegenerative disease. In-vivo neuromelanin imaging is a potential biomarker, but previously-developed approaches can be too lengthy for routine clinical use. Goal(s): To optimize the contrast of locus coeruleus (LC) and substantia nigra (SN) in a fast, segmented EPI readout variable flip-angle magnetization transfer (EP-vfMT) acquisition. Approach: Contrast of LC and SN were optimized as a function of echo time (TE), repetition time (TR), and MT flip-angle while limiting scan time to 5 minutes. Results: Optimal contrast was found by minimizing TE and maximizing MT flip-angle. Contrast was insensitive to TR. Impact: The speed of the proposed acquisition will enable examination of EP-vfMT as an imaging biomarker for early-stage neurodegeneration in Parkinson's disease, Alzheimer's disease and other neurogenerative disorders.