Transcranial magnetic stimulation (TMS) during positron emission tomography (PET) is a novel technique for in vivo measurements of connectivity and excitability of the human cerebral cortex. Here we describe tools that allow investigators to position the stimulating coil over a target region and to verify the actual position of the coil after the study. The former is achieved by coregistering the head of the subject with an MR image of his/her brain using frameless stereotaxy. The latter is accomplished by identifying the coil on a transmission scan and coregistering it, e.g., with a model of the electrical field induced in the brain.