Is there a way to apply a label to a mgh file? I would like to show a gray brain with values from an mgh shown only in the significant areas (ie only within my label). Is there a way to do this?

I have a set of mgh files with beta values from a regression. I also have a set of labels for the significant areas. Both sets of files were created in matlab and are in fsaverage space. I can open the two files together in tksurfer and see the entire beta map, along with the label for the significant regions.

Is there a way to zero-out all of values in the mgh overlay which fall outside of my label?

A command line option would be preferable, since I have several maps.

Thank you very much!