did you see Doug's earlier response to this question? On Fri, 30 Sep 2016, Ali-Reza Mohammadi-Nejad wrote:

Dear Freesurfer experts

Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface. Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH). Now this difference map is saved in a .mgh file. I think, I can use "mris_anatomical_stats" command for this propose. But, based on the help of this command, I did not find any .mgh file as an input. Therefore, would you please help me to create such stats file? Thank you very much for your help   Best regards, Alireza