Try making the preferences dialog bigger and see if it shows up.

If this does not work: Save the CT from BioImage Suite out and then use this version (i.e. the saved one) for registration. FSL may work better with this as, at least, it will be consistent with the electrodes. Otherwise send me a direct e-mail early next week (Xenophon dot Papademetris at yale.edu) and we can figure it out.