Once the solution has been found for the 4mm resolution, it is assumed that this corresponds to the desired solution and simple re-optimisation occurs at the 2mm and 1mm resolutions.
For the 2mm case, the optimisation is initially run with 7 then 9 then 12 DOF in order to iteratively improve the fit. Note that it is only at this resolution that anisotropic scalings and skews are included in the optimisation.
In the 1mm case, the computational burden is high, taking over 3 seconds for each cost function evaluation (compare this to around 50ms for a single evaluation at 8mm). Therefore, only a single optimisation pass with 12 DOF is run, in order to make minor adjustments in the transformation. Even so, this stage typically takes 10 minutes to run which is approximately 25% of the entire execution time.