I am just curious whether the mask.mgh file returned in glmdir folder created from lh.cortex.label?

If so, how can I create my own surface mask from the label file? (mri_label2vol and mri_vol2surf ?)

Second: How can I compare the subcortical volumes between the 2 groups using glm tools in freesurfer? Specifically, how do I call mris_preproc and mri_glmfit?

I appreciate your response. 

Thank you

Regards

--VM