Hello;
By my understanding, you need to be able to recognize different waveforms that will be divided up by counter pulses.
One thing you can do is, since you know the sample rate of your Analog Input operation, you can use a counter to measure how much time was elapsed in between two counter pulses, than do some calculations on your VI to determine the number of points per waveform, after retrieving all datapoints from the file.
So, the main idea is to stream to disk all Analog Input points, and also save the counter information to a different file, then, retrieve that information and post process both files to figure out the number of points per waveform.
Hope this helps.
Filipe A.
Applications Engineer
National Instruments