[Freesurfer] freesurfer transformation matrix

Dear all, I am an undergraduate student working in Dr. David Ress' lab at Brown University making a comparison of different brain segmentation applications among them freesurfer. However, I ran into much difficulty conducting a proper quantitative comparison of outputs. Indeed, I noticed that the data was shifted and possibly rotated in freesurfer. In order to superimpose the output by the different applications I must put all data back in its original coordinate system. I was wondering if there is a way of obtaining the transformation matrix used by freesufer. Thank you very much for your help. My very best regards, Akram.