You chip has one or more 16-bit timers. The first is Timer 1; the others will have sequential odd numbers. Timer 1 types can be set to trigger on either, both, or alternate edges of a pulse. You probably just want to pick either a rising or falling edge. Since your MCU will be running very fast relative to the pulse, you also need to pre-scale the counter (or its trigger) so you do not overflow more than once during a count. As 16-bits give you more than enough precision for your project, I would set the pre-scale fairly high.