this is a tough question since there is no real ground truth if you can’t see the contacts. You can try to adjust the contrast and brightness levels in the review window and try to see if you can determine the contacts. My experience is that one can see the single contacts better in mr images.
Another alternative is to double check in a different viewer after you have saved your reconstructions.
If you use Slicer in the version 3 (I have version 3 and 4 installed simultaneously on my computer), you can directly read in the .fcsv file Lead generates as fiducial points. You can overlay these points onto the image and adjust the contrast of the image better and more accurately in slicer than in lead. If you are lucky, you can see the single contacts there.
If you dont want to use slicer 3, you can also manually place some fiducial points in e.g. slicer 4 and enter the coordinates from the .fcsv or the ea_reconstruction.mat file manually.
I guess in general your heuristic is not quite wrong given the architecture of the electrodes and my own experience. I have analysed some patients that had both CT and MR postoperatively taken and could directly compare the results between MR and CT. Going ~4 steps up is at least a rough heuristic and the distances we talk about are probably quite small (i.e. within image resolution magnitude).
However, if you can’t really see all 4 contacts, you can also only guess how the spacing between the contacts changed due to the normalization procedure. If a patient’s anatomy is e.g. stretched a lot in z-direction to fit the template’s anatomy, the between-contact spacing of this patient within MNI-space should also be larger than the actual electrode spacing (e.g. 2 mm for most makes).
I hope this helps!