Hi,
Welcome to the forum.
Please read the first post in any forum entitled how to use this forum.
http://forum.arduino.cc/index.php/topic,148850.0.html then look down to item #7 about how to post your code.
It will be formatted in a scrolling window that makes it easier to read.
What is the application?
Are you counting pulses from an external source and want to gate them ON for a particular number of pulses or time.
OR
Are you producing the pulses in the DUE and gating them ON for a particular number of pulses or time.
Can you please post a copy of your circuit, in CAD or a picture of a hand drawn circuit in jpg, png?
Thanks.. Tom.. 