This article leaves out some of the detail from older articles (specifically [1]) about this patient where they describe the painstaking process by which they determined these patients were answering yes-or-no questions knowledgeably. See also [2] for an older article with more detail around the process.

[1] http://www.nbcnews.com/health/health-news/brain-scans-reveal...

[2] http://www.nytimes.com/2010/02/04/health/04brain.html?em

They rely on mental imagery [0] to communicate.

They ask the patients to imagine themselves playing tennis or wandering in their house for tens of seconds at a time. These tasks activate different neural networks, and it is possible to tell them apart using fMRI.

Sustaining the activation of higher level cortices requires not only consciousness but attention and concentration.

From there they can encode yes/no answers (tennis vs house).

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0. Detecting Awareness in the Vegetative State—http://www.sciencemag.org/content/313/5792/1402.short

Full text: http://perso.univ-rennes1.fr/pascal.benquet/index_fichiers/s...

This is the first publication with this protocol, which has been cross-validated and widely applied ever since: http://scholar.google.com/scholar?cites=16360852850070909865...

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