Dear Matteo,
That is a very interesting question I also recently discussed.
In the end we were wondering if it wouldn't be an option to construct a (flexible) divider between the eyes, through the middle of the head of the subject, all the way to the projection screen (which is attached to the MEG system). One could think of a partly plastic (straight-edged, connected to the projection screen), partly cloth or styrofoam (at the subject-side connected from forehead to chin) divider. The visual stereoscopic image could then be presented on separate left-right halfs of the projection screen. Can you imagine it (if not I will sketch it out)?
It would be great to hear of your thoughts on this, or to hear other options.
best,
Stephen