In the function AAM_align_data.m, you have chosen the base to always be the first shape. According to Procrustes analysis, isn't the base supposed to be the mean of the current set of aligned shapes? Am I missing something in your code or are you using some sort of modified Procrustes analysis which aligns all shapes to the first shape? If it is the latter how much difference would it make in the result?

Could you tell me how one selects the landmark points. And how do you set the coordinates of these points? Till now I was under the impression that the coordinates are the row and column indexes of the pixel in the image matrix. I saw x and y having values like 216.8761?
Secondly, for the database of training images, what are vector t and matrix I for? I understand x and y give the coordinates of each point. What are t and I?
This is my first project in image processing so I really have no clue.
Thanks in advance!