Douglas, 

I am looking at them in freeview and mango. They are not aligned. I am able to align them using flirt, and they come out perfect. I have tried 5 cases. 3 of them they are aligned, two were not. I am loading below the wm and lh.wm. They are supposed to be aligned (wm is aligned with T1). 

I got a surface by using Bruce's method, but it's much more irregular than the one obtained from mri_surf2vol. I wonder why the inconsistency. I guess I can create the surface and flirt using a solid transform to the T1. It takes longer, but it works. 

Gabriel