You are probably looking at the effect of brain deformation as a result of putting stuff in the brain.

The best procedure is:

Nonrigid mapping between preop MRI and postop MRI (we do this using stripped MRIs)
Rigid mapping between postop MRI and postop CT (use unstripped images for this one)

Then invert both transformation (the nonrigid one .grd will take a while) and concatenate them in the ElectrodeEditor transform Grid tool to move the electrodes back.

Xenios