There has been a recent lively debate on the hazards of functional magnetic resonance imaging (fMRI), and what claims to believe or not in the scientific and/or popular literature [here, and here]. The focus has been on flawed statistical methods for assessing fMRI data, and in particular failure to correct for multiple comparisons [see also here at the Brain Box]. There was quite good consensus within this debate that the field is pretty well attuned to the problem, and has taken sound and serious steps to preserve the validity of statistical inferences in the face of mass data collection. Agreed, there are certainly papers out there that have failed to use appropriate corrections, and therefore the resulting statistical inferences are certainly flawed. But hopefully these can be identified, and reconsidered by the field. A freer and more dynamic system of publication could really help in this kind of situation [e.g., see here]. The same problems, and solutions apply to non-brain imaging field [e.g., see here].
Evil 2: Flawed inference, period.
Whatever our statistical test say, or do not say, ultimately it is the scientist, journalist, politician, skeptic, whoever, who interprets the result. One of the most serious and common problems is flawed causal inference: "because brain area X lights up when I think about/do/say/hear/dream/hallucinate Y, area X must cause Y". Again, this is a very well known error, undergraduates typically have it drilled into them, and most should be able to recite like mantra: "fMRI is correlational, not causal". Yet time and again we see this flawed logic hanging around, causing trouble.
There are of course other conceptual errors at play in the literature (e.g., there must be a direct mapping between function and structure; each cognitive concept that we can imagine must have its own dedicated bit of brain, etc), but I would argue perhaps that fMRI is actually doing more to banish than reinforce ideas that we largely inherited from the 19th Century. The mass of brain imaging data, corrected or otherwise, will only further challenge these old ideas, as it becomes increasingly obvious that function is mediated via a distributed network of interrelated brain areas (ironically, ultra-conservative statistical approaches may actually obscure the network approach to brain function). However, brain imaging, even in principle, cannot disentangle correlation from causality. Other methods can, but as Vaughan Bell poetically notes:
Perhaps the most important problem is not that brain scans can be misleading, but that they are beautiful. Like all other neuroscientists, I find them beguiling. They have us enchanted and we are far from breaking their spell. [from here]In contrast, the handful of methods (natural lesions, TMS, tDCS, animal ablation studies) that allow us to test the causal role of brain function do not readily generate beautiful pictures, and perhaps, therefore suffer a prejudice that keeps them under-represented in peer-review journals, and/or popular press. It would be interesting to assess the role of beauty in publication bias...
Update - For even more related discussion, see: