Michelangelo was at continuous odds with his employers during his lifetime, he dissected corpses illegally at first, later with tacit approval of some of the church bigwigs in order to improve his skills as an artist. It was a continuous give-and-take to see who got the most out of the arrangement.
In the end I think we, the future dwellers able to see his work no matter what caused them to come into being are the real winners.
Not bad for a man who declared himself unfit to execute the work because he was a sculptor, not a painter...
There is a very good book about him that I forgot the title of (I read it ages ago).
Wasn't it more like "declared painting as unfit for him"? Michelangelo had a strong disdain for paintings and painters especially Leonardo Da Vinci and his friends.
My only source is [this biography](1). Not sure how accurate that is.
[1]: http://www.amazon.com/The-Agony-Ecstasy-Biographical-Michela...
The "standard" sagittal section as in this image (i.imgur.com/ZTvy55n.jpg), or this image (i.imgur.com/73YdDXa.jpg) is chosen precisely because it shows in one image several important features of the brain, and is also recapitulated nicely by MRI images, as you mention.
However, there is no reason why Michelangelo would know anything about the different regions of the brain and therefore choose a representation that showed them.
A "fresh" human brain (which is what Michelangelo would have seen) looks like this (i.imgur.com/KXBLtrx.jpg), or this (i.imgur.com/Bm5l8n6.jpg), and without further dissection do not look much like his paintings.
Such brains can be further sectioned in any number of ways, none of which are necessarily obvious. The question then is would Michelangelo have dissected brains in the same way as is now done?
The inside of the skull is not shaping the skull in a way that it will come out 'wrong' if you don't know about what's in the skull.