The neocortex consists of excitatory and inhibitory neurons, each playing distinct roles in brain function, and the loss of their integrity contributes to various brain disorders. Optogenetic neuromodulation combined with functional magnetic resonance imaging (opto-fMRI), intracranial electrophysiology, and tract-tracing histology enables comprehensive monitoring of neural activity across the whole brain and spinal cord. These techniques can be used to derive causal connections and quantify both functional and anatomical connectivity within and between networks. To date, while most opto-fMRI studies have been conducted in rodent models, the number of optogenetic studies in non-human primates (NHPs) has grown rapidly. Given the greater complexity of brain and spinal cord circuits and neuronal types in NHPs, which more closely resemble those in the human brain and spinal cord, opto-fMRI in NHPs presents unique technical challenges. Nonetheless, it represents a crucial step toward potential human applications, especially as the technology continues to advance. This approach has proven especially valuable for dissecting the neural circuits underlying complex behavior and for providing new insights into the brain’s functional architecture—from specific neurons in particular brain regions to large-scale functional and anatomical connections. In this chapter, we focus on the technical considerations involved in conducting optogenetic fMRI, electrophysiology, and anatomical tracing studies in an NHP model system.