Hi there @polminuts,
I imagine you have already solved your problem, but in any case, you might have look to tc_lib for measuring a digital signal using timer TC modules available in DUE's ATSAM3X8E microcontroller. You can find the library here: https://github.com/antodom/tc_lib.
@HermannSW has done some nice work measuring tc_lib's limits in this post: here
I hope it helps.