Establishing connection patterns between cortical columns is essential for understanding human brain networks. However, currently, there is no method to systematically map at this sub-millimeter scale. Here, we combined pulsed infrared neural stimulation (INS) with high field fMRI. Applying this method in cat and monkey brains, we found that single site INS stimulation produces reproducible, intensity-dependent activation. Our experiments revealed (1) connections between cortex and subcortical locations, (2) long-range cortico-cortical connections, and (3) local cortical connections. We suggest that INS-fMRI is a new in vivo functional tract tracing technique that can map networks with high spatial resolution.