I think the reason to use 'a' here is to account for the knowledge of the reader, and is thus correct.
The brain region called 'x' ...
the writer assumes that the name of the brain region explains what is specific about this brain region. However, the average reader of this article is none the wiser if he knows the name of the brain region. An alternative phrasing would prove this:
The 'x' brain region ...
This will leave the reader wondering "What 'x' region? I don't know such a thing!". So, if 'the' is used, the reader will expect some more information; e.g.
The brain region called 'x', located near your ears, ....
Compare with AllanaRose's answer, which explains that you can only use 'the' when the object is specified later; in this case, although 'x' does specify the object gramatically, it does not provide relatable information to the average reader.
A brain region called 'x'
this could be read as
Some region called 'x'
This shows the writers intent not to explain anything about this brain region; he just puts the name of the region out there, and shows that, even though he could specify exactly what this region is all about, he chose not to.
Edit: since this is the language learning stack, I ought to add that 'the' is acceptable as well. This question may have been better fit at the English Language usage stack...