Hello Sam,
I'm not quite sure what you are trying to measure. If you are trying to measure an analog signal could you use a 1ms delay using the delay function in LabVIEW and then start an acquisition that acquires data at the upper rate (10kS/s) for 2 samples? If you are trying to measure a digital signal, it will have to be entirely timed in the software. If you are trying to use the counter to do a timing measurement, this is not
supported by the hardware. Tell us a little bit more of your application and what you are trying to do and we can offer you some more advice!
Eric
DE For Life!