Please keep in mind that registering a brain image to an atlas whose brodmann areas have been outlined does not mean that you have established Brodmann areas in your registered brain.  All that registering two brain images together accomplishes is to make them appear similar to one another, and in doing so, we hope that the image similarity reflects anatomical correspondence across the brains.  To further expect that microstructural boundaries follow macrostructural boundaries (that is, histology has a consistent relationship to topography) is still unsubstantiated in my opinion.  Furthermore, most atlases that have been assigned Brodmann labels were never examined under a microscope, so the cytoarchitectural regions even for these atlases are often suspect.  

Be careful!

Cheers,
@rno