Atlas anatomy terminology and other anatomical notations

Hello everyone,

I have been trying to find an accurate mapping between several brain areas, some of those named after their function, and I find it a tremendous difficult task and perhaps with uncertain results.

Being more specific I can provide an example:

What would be the best map of the following area: “Brodmann Area 3a: primary somatosensory cortex”
The closest I have found is the postcentral gyrus and further more I have no means to break this large area into smallest subregions. This is because I have no confidence in mapping further down to the hierarchy with the inferior bank etc. I believe this is because these terms, inferior, superior bank are not in correspondence with the terms anterior, posterior, ventral dorsal, medial temporal.

Any help with will be greatly appreciated, please don’t hesitate to point where I am missing something.



Hi Eleftheria,

I don’t know the answer to your question, but a good place to start would be at our Allen Brain Reference Atlases page at There is both a Gyral and a Modified Brodmann atlas which you can overlay in the same image. For example, if you start at this link you can change the “Alternate Background Image” (the rightmost dropdown box in the upper right corner of the screen) to “Cortex - Gyral”. Hopefully, this will at least get you pointed in the right direction.


Hello Eleftheria,

Thank you for reaching out to us regarding your question. There is a function within the interactive atlas viewer Jeremy is referring to that should allow you to determine the area of interest rather neatly. Here’s how it works:

  1. Open the Human Brain Atlas Guide:
  2. Engage the second dropdown seen in the upper right corner of the window (next to the 3-bar settings icon) and select “Cortex – Mod. Brodmann”. This will show an “underlay” of the BrainSpan Atlas which was specifically delineated indicate Brodmann Areas for comparison with the Human Brain Atlas (and vice versa).
  3. If you hover the cursor over the image in this mixed view, say over S1C (our acronym for primary somatosensory cortex, in bright orange), you will notice the acronym shown in the upper left of the interactive window will indicate “postcentral gyrus left” (except for the little bit on the on the bottom where it says “precentral gyrus, left”). This may be used to make judgements about functional and landmark areas
  4. You will also notice solid lines and faint lines which show where landmark areal regions (gyri designations) differ from Brodmann Areas. Obviously there are many places where this occurs.

Hopefully that will enable you to cross reference functional and landmark designations in human cerebral cortex.

If you are really more in need of just a Brodmann map, you can also just skip the overlay-comparison method above and just use the Cortex-Mod.Brodmann map on its own. To do that, engage the left dropdown, find “34 yrs, Whole Brain” and select “Cortex – Modified Brodmann”. Or follow this link:

As “Area 3a: primary somatosensory cortex” was used as an example on a broader question about atlas usage, I won’t go into answering that here. Please write back if you have any need to discuss the anatomical analysis of this specifically.

Hope that helps,



Thank you Josh for thorough guidance. If one is interested in MNI co-ordinates of brain subregions, is the Human Brain Atlas Guide providing them?



Hi Eleftheria, thank you writing!

Assuming you’re using the Allen Human Brain Atlas (HBA) Guide because of HBA data, I recommend using the MNI coordinate space in the viewing tool ( or, if more is needed, separately register the MRIs from HBA brains of interest to your preferred MNI coordinate space. From there you can match anatomy by eye with the Human Brain Atlas Guide. We do have an MRI for the 34 yrs, whole brain atlas, which in theory might allow anyone to ascertain coordinates for all the adult human atlases in the link directly, but it doesn’t register to MNI. One thing you to might be happy to hear is that we’re currently in the process of building a 3D Human Common Coordinate Framework based on the MNI/ICBM-152 average template using the 34yrs, whole brain ontology. This will enable reference atlas delineations to skin to this standardized MRI volume average and thereby anatomically inform anything registered to it.

Should you need help translating ontology terms between the Human Brain Atlas Guide and the 34 yrs, whole brain atlas, please let me know. Moving forward, all human data is expected to utilize the latter’s ontology.


Dear Josh,

I am sharing the information provided with my fellows, one question they have is when the framework you are currently building will it be done?

Thank you for being so helpful

Best regards,


Hi Again,

At this point I would say check back with us at SfN (should you or any of your fellows be in attendance) or visit our website at the beginning of next year. Much deliberation on scope of final anatomy and delivery mechanism(s) is happening at the moment and we should have more to report later in the year.