External trigger and timer use

Hello to the forum , this is my first message.

I am trying to achieve a simple task of accurate time measurement between 2 pulses applied to 2 pins of the due board.I am struggling with the sam3x manual right now but there is too much info and i got confused for the moment.

I am not sure if i understood well but i think that it is possible for sam3x to automatically start a counter when an external interrupt is sensed, without calling a software interrupt routine.

So i need to start a counter when the voltage is rising on inputX and stop the counter when the voltage is rising on inputY . Then i need to access the counter value . The time interval is a few milliseconds so i need the timer set to MCLK/2

Any help is much appreciated.