MATLAB - stereoscope depth calculation

I have sourced codes and a calibration camera toolbox for MATLAB however I am having trouble understanding it/ getting it to work properly. What I am after is for MATLAB to analyse pairs of photos so that i can measure distances from the camera using stereoscope technique. This paper i found outlines it all however i am struggling to understand it all.

As the paper is to big to upload here is the link:
http://archives.njit.edu/vol01/etd/2000s/2008/njit-etd2008-017/njit-etd2008-017.pdf
The toolbox:
http://www.vision.caltech.edu/bouguetj/calib_doc/