As it happens for cortical surface mapping I would like to obtain the same for subcortical structures. I have generated the subcortical surfaces using fsaverage brain’s aseg.mgz with the tool given in: https://github.com/thomas-vincent/nipic/wiki/%5BFreesurfer%5D-Get-surfaces-of-subcortical-structures

With this I would like overlay data on them. I have used mrf_vol2surf command 

as my overlays are in MNI space. However, I am not able to overlay these on the surface. I think this is because the data file that is generated (lh.sub_me_c_surf.mgz) hasn’t got the same number of vertices as the subcortical generated surface (163842 vertices of the overlay file to 37722 vertices of the surface file).