Modern neuroimaging promises to transform how we understand human brain function, as well as how we diagnose and treat mental disorders. However, this promise hinges on the development of computational tools for distilling complex, high-dimensional neuroimaging data into simple representations that can be explored in research or clinical settings. The Mapper approach from topological data analysis (TDA) can be used to generate such representations. Here, we introduce several improvements to the underlying algorithm to aid scalability and parameter selection for high-dimensional neuroimaging data. We also provide new analytical tools for annotating and extracting neurobiological and behavioral insights from the generated representations. We hope this new framework will help facilitate translational applications of precision neuroimaging in clinical settings.