B grid spline optimisation

physical101

Dear All

Firstly thank you for looking at my post. I am trying to nonlinearly warp an image with respect to another using a free form deformation. I am trying to code the following paper in matlab:

http://www.cs.jhu.edu/~cis/cista/746...mBreastMRI.pdf

I understand most of the implementation but was left confused about how to optimise the deformation of the spline control points. In the paper grid points are moved in order to minimise a mutual information metric, I am using simple overlap minimisation but the procedure should be the same. Can you really optimise 3000 variables? Or have I missed the point entirely.

Hoping you can help

Physical101