a few thoughts:
1. did you normalize the subject before? It won’t work otherwise. Which normalization method did you use? ANTs?
2. does visualization of the atlas in MNI space with the electrodes work okay?
3. Is it an “official” atlas or a custom one you made? If the latter, please try visualizing a different atlas first.
4. Which OS do you work on (Win/Linux/Mac) and what Matlab version do you use?