Brain atlases commonly used for characterizing neurodegenerative processes are frequently referenced to a specific imaging modality. Here we describe a combined gray matter and white matter atlas to be used in the study of a rhesus macaque model of Huntington’s disease. We illustrate how this atlas will be used to integrate diffusion tensor imaging and resting-state functional MRI connectivity with measures of cognitive behavior. Prefrontal WM tracts, cortical and basal ganglia regions are labeled in the same space for characterization of WM microstructure changes and cognitive and motor loop connectivity. The results of preliminary study show that these MRI measurements can identify correlations with cognitive behavior measurements.