You can simply count the clock cycles between two interrupts in the following way (I am explaining step wise):

1. Define an integer (2 bytes register) and initialize it with Zero.
2. Run any timer for about 1ms interval
3. If one interrupt arises reset that timer and on every timer overflow start incrementing an integer.
4. As soon as the 2nd interrupt arises, stop the timer and check the integer value.
5. Use the integer value anywhere u want and reset its value to Zero again.

Maaz Qazi