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 

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