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Dear Stephen and Antoine,
thank you for the much appreciated feedback.

I found this paper (http://bit.ly/14PwH8x) that describes how to build a
MR-compatible stereoscope, and I was thinking to give it a try. The idea is
simple but ingenious: instead of using mirrors it adopts prismatic lenses
and a divider. I haven't talked to an optician yet, but I guess these
lenses can be created with any form, and then one can easily use the
MEG-compatible glasses.

The only limit I can think of is that the prismatic distortion is fixed, so
one can adjust the horizontal alignment to fuse the images only by changing
the position of the stimuli on the screen. But if the distance between the
subject and the screen is fixed, then this should be sufficient for
inter-subject differences of eye distance. One added benefit of this option
is that one should be able to use an eye-tracking system as well. The main
drawback might be the cost of the lenses.

I would like to hear your thoughts on this.
Thanks!
Matteo