Hi Diego
I am not really sure what you mean by “completely ignore the cortical grayordinates”?
The command --surface-apply-warpfield will transform the coordinates of the input surface to the target space of the warp. The warp you are using is non-linear and goes from a single-subject native space to a group space which is a very different space. I would not expect the transformed surface to look as smooth as the original surface…
It is not obvious to me from these images that this is a problem. What would you be expecting the transformed surface to look like?
Cheers, Sean