If you have two similar signals, you can use the NI-SCOPE measurements to get either the phase or time delay between them. Set up the NI-SCOPE digitizer with your input wave in channel 0 and output wave in channel 1. After a successful acquisition, set the Waveform Measurement->Other Channel attribute to the channel 0. Use niScope Read Measurement.vi on channel 1 to take the measurement. This assumes your are using LabVIEW. The C/C++ procedure is essentially the same.