A method of affecting a biological, cellular or biochemical function or structure in a targeted subcortical location in a brain of a patient using a TRPMS apparatus placed on a head of the patient includes positioning two or more of a plurality of magnetic assemblies on locations of the head mount selected to stimulate the targeted subcortical location in the brain of the patient, and activating the plurality of magnetic assemblies at the selected locations to generate magnetic fluxes of a selected strength, frequency and duration directed into the brain of the patient, wherein the magnetic flux directed into the brain of the patient from each of the assemblies is operative to generate induced electric field in regions of the brain and the regions of induced electric fields generated by each of the plurality of magnetic assemblies converge in the targeted subcortical location and combine to a magnitude sufficient to affect the biological, cellular or biochemical function or structure in the targeted subcortical location.