Q: I’d like to try to use some anatomically shaped (and morphologically dilated) masks to refine an affine registration into a piecewise affine registration. I’m seeing however that my objective function with minctracc starts off with a null objective function, for middle ear registration, and therefore produces the same transformation as its starting point. Is it possible to make its computation a bit more sensitive than it is?
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2008-January/001888.html

A: I presume you mean you are aligning a mask to another mask? If this is the case yes you will have a fairly “saturated” objective function.

I would suggest using something like mincmorph and do a distance transform on both of them and then align that.

The other option would be a mincblur with a big FWHM.