Hi Rick,
> Regarding your first question about 3dAFNItoNIFTI, would you
> upload that? It would be helpful for us to reproduce it here.
I uploaded a file "nickoosterhof_3dAFNItoNIFTI_problem_June2009.zip" with an anatomical that gives me the problem.
> Regarding the anat_al+orig and SurfVol+orig alignment, it seems
> likely that the 3dAllineate matrix is the inverse of what you
> want to apply, meaning you should use -ixmat_1D instead of just
> -xmat_1D.
I tried both, and neither works. With -xmat_1D the surface is off up to about half a centimeter (and the angle is off, too), while for -ixmat_1D it is a couple of centimeters.
Thanks for having a look at it!
best,
Nick