Did you visually check the registration of the functional to the
structural?
The registration using tkregister2 produces three files func2struc.mat func2struc.hdr func2struc.img,
I've tried to load func2struc.hdr in TkSurfer, but it crashes. Again, I don't understand what you do when you "visual check" registration. I am new to fMRI, please be more specific.
Thanks. Nam.