Couldn't you use YAAPT instead, which has been implemented as a matlab function? Seems that Yaapt is superior to the RAPT method (e.g. http://www.ws.binghamton.edu/zahorian/yaapt.htm). Matlab should be easy enough to automatize your measrurements. Best X.
Thank you very much for your suggestion mr. Koch. I'm going to try YAAPT as well, but I still need to test RAPT. For now, I'm going to test it in a few signals.