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Using a 32 bit timer to calculate time difference between 2 seperate interrupts

Hi,

  I want to use one of the 32 bit timers on the 6748 to calculate the time difference between 2 seperate interrupts.  The time difference needs to be within 10's of ns.  I configured Timer1 to be 32 bit unchained continuous.  I set the period for max value.  I set up the timer to reset when TIM12 is read.  I read the TIM12 register, perform 3 NOP's and then re-read the TIM12 register again and the values don't seem reasonable.  I am using SYS/BIOS.  Basically I want to be able to clear the clock counter.  Start the clock counter when I receive the first interrupt and then stop and read the clock counter results when I receive the second interrupt. 

Thanks,

Will