We have previously shown that INS-fMRI is a rapid method for mapping mesoscale brain networks in the macaque monkey brain. Here, we extend this capability by stimulating deep brain sites. We test this new method by stimulating the basal nucleus of amygdala in the macaque monkey. The connections we identified are consistent with dye-tracing studies. In conclusion, our results indicate that INS-fMRI is a promising novel method for mapping connections of deep brain structures at high spatial resolution.