I do not believe there’s any way you could actually feel lesions in your brain - the brain isn’t sensitive to touch, because normally, there’s no way it could get touched, as it’s in a sealed container - LoL. So it just doesn’t have that capability. People have actually had brain surgery whilst conscious, and don’t report that it’s painful. Obviously, getting through the skull to get to the brain presents more of a challenge to the anaesthetist, but the brain itself doesn’t feel.
I haven’t had the exact symptom, but is it definitely your head, and not, perhaps, your ear? I get popping in my ear sometimes. I believe there’s a tiny little muscle in there, that can go into spasm, just like other muscles do with MS. When this happens, there’s like a beating or popping sensation - I’m not really sure if it’s a feeling or a sound. Sometimes it feels like there’s a moth trapped in there. It’s very annoying, but not painful.
Other than that, I don’t know. Maybe do mention it to the nurse or neuro next time, as they might have some ideas? But if it’s only occasional, and lasts just a few seconds, would you want treatment for it anyway? I don’t think I’d want to take drugs all the time for something that only happens now and then, and lasts seconds. If your main concern is reassurance it’s not dangerous, they may be able to provide that.