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I have long had interest in dreaming, and one of the defining features of ordinary dreams is that the dreamer either accepts the dream as "real life", or does not question the surroundings.

Compare these ordinary dreams with "lucid dreams", or conscious dreaming, where the person is aware of the fact that he/she is dreaming. Within an ordinary dream, a person "goes with the flow", while within a lucid dream, the person can think clearly and act voluntarily without waking up.

Have these been any studies that used fMRI or other techniques to try to determine what is it within the human brain that causes the distinction between conscious and ordinary dreaming?

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I think from a practical perspective it's difficult to get someone into a comfortable sound sleep in an MRI machine. –  Chuck Sherrington Feb 7 '13 at 4:28
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[I'm perhaps in the minority here.] I had thought the title meant "What causes people to accept recalled dreams as reality?" until the description of the question cleared that up for me. Nothing in the title presently indicates or implies that the acceptance occurs during the dream. Maybe rephrase the question "What causes dreaming people to accept their dream as reality?" or "What prevents dreaming people from wondering if they're dreaming?" –  John Pick Feb 7 '13 at 22:30

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up vote 4 down vote accepted

If you are searching specific part of the brain, I think that frontal regions of cortex will be an answer(In particular, the dorsolateral prefrontal cortex which was associated with self-focused metacognitive evaluation). But, as it common in real life, becoming aware of dreaming state required coordinated work of different parts of brain. You can read this very good article and wiki of course.

Lucid dreaming is characterized by a regaining of higher cognitive capabilities, eventually leading to the awareness of the dreaming state. Recent quantitative EEG data have shown that this wake-like intellectual clarity is paralleled by neural activations in frontal and frontolateral regions. Likewise, PET data show cognitive control in dreams to be associated with activation of frontal cortex components. via

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Also this article is interesting –  sviter Feb 7 '13 at 18:35
    
Great link. From the article: " During lucid dreaming the bilateral precuneus, cuneus, parietal lobules, and prefrontal and occipito-temporal cortices activated strongly as compared with non-lucid REM sleep." –  Alex Stone Feb 9 '13 at 5:13

Probably just a part of the story, but the locus coeruleus is known to be implied in the wake-sleep cycle.

Furthermore, an experiment on cats demonstrated that removing this structure cause actual (but nonsensical) behaviors replacing normal REM sleep phases: cats have no more REM sleep and instead hunt non-existing rats (or something else who knows).

http://psycnet.apa.org/psycinfo/1980-27526-001

However, that does not mean that people with confusion have a lesion of this this structure.

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