Hi Ali,
Thank you for posting this. My recommendations are going to be closely related to the answer I gave to another recent question of yours.
You won't be able to use two separate USB microphone to estimate inter-microphone delays as your OS will most likely inject unpredictable latencies, different at every acquisition. Instead, you should get your hands on a multichannel audio interface, preferrably with ASIO drivers - anything from a simple 2-channel consumer sound card to a high-end multichannel interface.
That type of configuration will ensure your two separate channels are acquired synchronously. When using audioDeviceReader, make sure that the value of SamplesPerFrame is the same as the value you set in the Buffer Size/Length in the ASIO configuration panel of your sound card. That panel is now also reachable directly from MATLAB via the function asiosettings .
Ragards,
Gabriele.
