afni.nimh.nih.gov

That is not one of the guided processing steps,
but maybe it should be, particularly when using
non-linear registration to the template.

If your processing script used the TT_N27+tlrc
template (as is the default), they should align
pretty well.

But note that in the case of affine registration,
the gyral contours will almost certainly not align
well, as the brains are from different people.
Look for a reasonable, gross alignment in the
affine case.

- rick