A method and device provide simplepositioning of a TMS coil relative to a coordinatesystem of the patients head while allowingflexible positioning of the patients head. Thesystem includes a mobile console on a wheeled basethat integrates various subsystems and supports amast that, in turn, supports a coil gantry thatsupports a TMS coil assembly. The coil gantryincludes a balance arm with a counterbalance and ahalo assembly that connects to the coil. The coilgantry supports the weight of the coil and allowsfree movement of the coil in all dimensions for easyplacement on the patients head. A head supportand coil alignment unit includes several parts thatare designed to provide maximum patient comfortand reliable coil position measurement of thepatients motor threshold (MT) location and TMStreatment location.