I would hazard a guess that they are also trying to find truly neutral question, that gets the same response by both groups.

So you can ask a neutral question and see if the same part of the brain is used in both groups.
Then ask a question they disagree upon and see what part of the brain lights up like a Christmas tree.

Also do atheist use the same part of the brain to answer
Can pigs fly?
Can Jesus fly?

What part of the brain do xtians use to answer yes to the second question.

Can Alexander the great do miracles V can Jesus do miracles?

Also as fair as I understand survey it's also important to ask a few reset question in between the real question.

If I ask you 10 question about the state of world poverty and human suffering then ask how happy you are feeling, you might be getting skewed answers on the last question.