The increased availability of high-field Magnetic Resonance Imaging (MRI) systems, genetic vectors, and molecular biological tools enables a more highly resolved study of deep brain circuits. These circuits - including monoaminergic (e.g. serotonergic, dopaminergic, noradrenergic) and neuropeptidergic (e.g. oxytocinergic, vasopressinergic) systems - are prominently involved in numerous neurological and psychiatric disorders, and are key mediators in swaths of nonvolitional phenomena in the healthy brain. The preparatory procedure for experimentally probing the aforementioned systems involves physical delivery of genetic vectors and/or signal input to deep brain structures. As target sites become increasingly well resolved, and advanced imaging equipment imposes additional spatial constraints, naı̈ve atlas-based structure targeting becomes less feasible. We present an integrated software and bench-workflow solution, which allows offline and animal-specific MRI-guided targeting of deep brain structures. We document the method’s capabilities on the basis of data demonstrating a cryogenic-coil compatible slanted targeting of the Dorsal Raphe (DR) nucleus for optogenetic functional MRI (opto-fMRI).