A system for delivering drugs or other molecules to the brain comprises an ultrasound imaging transducer configured to image structures such as the circle of Willis within a patient's head by way of a low attenuation acoustic window. The system includes a processor configured to register the ultrasound images to previously obtained images which also include the structures. The system includes ultrasound transducer elements operable to deliver ultrasound energy to a target region to cause the blood brain barrier to open. The system may include a drug delivery system that may be operated to deliver a drug to the patient in coordination with opening the blood brain barrier, Coordinates of the target region relative to the ultrasound imaging transducer are determined using registration information.