Hi Bruce,
I've grabbed the dev version
freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
and tried
mri_morphology <input vol> fill_holes 26 <output vol>
but got the message that the operation "fill_holes" is not supported.
Ed