Subject system generates high energy short duration repetitive magnetic fields controlled by a programmable pulse generator. The magnetic fields are applied to a patient's body through a smart coil attachment provided with a sensor system and microcontroller for monitoring the system's health. The novel security architecture and networking components support the electronic prescription concept which ensures a patient receives correct treatment on the prescribed pulse generator with the prescribed coil attachment. An FPGA-based pulser controller operates to control charging of large capacitors (in the pulse generator) to a desired voltage and discharging them through the smart coil attachment to generate the therapeutic magnetic pulses in accordance with the electronic treatment prescription protocol.