Neurodevelopmental disorders affect many aspects of brain function, and surveying phenotypic abnormalities across altered brains can be challenging. Our group has created a suite of novel tools that can probe molecular-level hallmarks of brain function by magnetic resonance imaging (MRI), potentially enabling qualitatively new and mechanistically informative approaches to the analysis of brain-wide dysfunction in autism and other conditions. Here I will present our recently developed molecular imaging approaches for mapping spatiotemporal dynamics of diverse neural signaling components, including dopamine release and calcium signaling. Initial application of these tools has taken place in rodents, but we expect our molecular imaging methods to be of outstanding utility for whole-brain functional analysis of emerging primate disease models. I discuss progress toward establishing fMRI in awake marmosets at MIT, with the future goal of applying novel functional and molecular imaging techniques to characterize marmoset models of autism spectrum disorders.