Provided herein are methods related to identifying an early, asymptomatic (prodromal) stage of a neurodegenerative disease or identifying a subject with a symptomatic neurodegenerative disease, including, for example, mild cognitive impairment (MCI), Alzheimer's Disease (AD), or HIV-associated neurocognitive disorder (HAND), using functional MRI data from the subject. Methods are also provided for treating a subject identified with the methods taught herein and for modifying or selecting treatment based on the results of fMRI. Methods are also available for staging neurodegenerative disease and for identifying agents useful in treating them.