Hi Boris,

For now I am taking the geometric average between pial and white surface coordinates.  

Is that the right way to do it, or is there a more precise way? 

To obtain a surface that lies in the geometric middle between white and pial surfaces, it is correct to take the average of the coordinates. This surface is not guaranteed to coincide with any biologically meaningful cortical layer, but it has advantages over pial or white for not over/under-representing gyri or sulci.

Also: If I decided to represent the stuff on the mid-surface, would it then also make sense to also take the average of pial.avg.area.mgh white.avg.area.mgh as the area estimation at each vertex? 

No no, to take the average of the areas is not the same as take the average of the coordinates, because the areas depend quadratically on linear distances. An average of the areas would not necessarily represent a surface at the middle, most likely representing an (invisible) surface that would be closer to the white in some places and closer to the pial in others, depending on local folding.

Hope this helps!

All the best,

Anderson