I am using the electrode editor for several months without problems now. But I remember similar problems in the beginning. Usually I did localize the electrodes in the original CT, not the coregistered one. My recipe to visualize electrode grids is the following:

1. Make sure you coregister the low resolution image (CT) with the high resolution image (MR). The high resolution image should not be changed.

2. Make sure the original CT has a different name than the coregistered CT. I do append "_coreg" to the name of the coregistered CT.

3. Localize the electrodes in the coregistered CT (i.e. *_coreg). This is the most important step!

4. Extract the brain from the original MR.

5. Load the extracted brain from the original MR into the electrode editor.

Now the position of the electrodes should match the correct positions very well if (!) the original MR was a post-OP image. Because in this case the effect of a subdural hematoma (a locally "squeezed" brain) will already be taken into account. In a pre-OP MR image the electrodes would appear a bit below the surface.

Just a last remark: I use FSL/flirt for step 1 and FSL/bet for step 4.

I hope this helps,

Markus