Yes, it would be difficult, given the digital nature of the signal.
The sketch should read something like this:
initialize the timer but don't turn it on yet
wait for the signal to go low; //assuming you are starting with falling edge
//now the signal has gone low
turn on the timer; //counting starts now
while (n) continue; //wait until the desired number of cycles have passed
stop the timer; //now the number of cycles has passed
read the counters;
Now, this approach is essentially polling so if you have other timing sensitive tasks, it will not work.
In that case, you can turn the whole thing into an interrupt drive approach - the same basic thought process.