> I have always used BIS to coregister CT/electrodes to (unstripped) MRI. It
> works great. It will solve your problem. You can threshold the CT to
> extract the electrodes as outlined in the manual, and touch up with editing
> any trouble spots in another program (I use MRIcron).
>

The only problem with CT and BIS is that an extremely large file will crash
the program (maybe memory allocation issue?), in which case you may need to
scale the CT down first.

I think your trouble could lie in the file format you use. FSL likes to
save in nifty, and BIS in Analyze preferentially, and the 2 programs may
interpret the headers differently.

If I do create a mismatch in orientations for some reason (the images are
still coregistered), I find it easier/more intuitive to "correct" that in
Amide than in BIS. Amide has pretty simple rotations (just invert the axis
as needed), but an arcane interface.

If you have 2 volumetric CTs, one with electrodes and one without, a nice
method to extract electrodes is to "subtract" the one without from the one
with.