The primary goal of my thesis was to address my hypothesis that: there is preferential perfusion of the hindbrain regions, controlling autonomic function. To test this hypothesis I developed a system for delivering hypoxic challenges to volunteers while they were in the MRI. I developed NIRS protocols that allowed monitoring of the cerebellum. And I developed MRI methods that allowed for PC MRI to be used to monitor flow to the forebrain and hindbrain. Finally I combined these elements to investigate how the brain would react to hypoxia. Ultimately neither NIRS nor MRI detected systematic differences between the forebrain and hindbrain response to hypoxia but the developed methods are available for future studies that aim to explore the hemodynamic response in the developing brain or in adults with pathological conditions.