One grand challenge of the twenty-first century is to gain a holistic understanding of neural circuits and their spatiotemporally coordinated patterns of neural activities that underlie brain functions. Neural oscillatory activities in the brain, particularly in the thalamus and cortex, are widely considered to mediate critical brain functions, such as memory consolidation during spindle activities (i.e., 0.5–3 s brief oscillatory events at 7–15 Hz). However, it remains unclear where such oscillatory activities propagate across the brain and, more importantly, their sites of multi-scale actions to mediate sensory or cognitive functions. This barrier precludes our existing frameworks from describing the exact roles of these oscillatory activities in functional processes. Here, we provide a multi-scale multimodal neuroimaging protocol that integrates small animal optogenetic fMRI with electrophysiological, behavioral, genetic, and molecular assays. This approach permits comprehensively interrogating where and how spontaneous neural oscillations causally act across brain-wide networks to support brain functions at the systems level.