How "Retrospective Image Registration Evaluation" works?

Hello everyone,

I have written my own multi-modal image registration program and now I am trying to evaluate it using different methods. I came across to "Retrospective Image Registration Evaluation" - RIRE - by Fitzpatrick. I read the articles about it, but it is still vague for me. I have found some MATLAB code in this link but I am confused how to use them. I would be thankful if someone could help me about it. Thank you.