Sorry, no experience with HRTIM.
For a standard timer, you would either use another timer as counter, and combine the two timers in some suitable maser-slave mode (you need timers with SMCR register, but most of them have...).
Or you would operated the timer in gated mode (again SMCR necessary), and then use another timer to generate the gate pulse the with correct length (thus this other timer then running VERY slowly...).
