AFNI Atlas Segmentation Question

Hello all,

I’m working on creating a standard set of MNI ROI structures for our lab and have a few questions about the way that AFNI handles atlases:

  1. I see that several atlases in AFNI are probabilistic. In FSL, these atlases are either thresholded at 0, 25, or 50. I was wondering if AFNI thresholds the atlases or if they are all thresholded at 0? I understand that given that atlases can be added, that this answer may differ by which atlas you’re using. So is there a way to tell the threshold of the atlas (if there is one?). I’ve tried 3dinfo and cat on the HEAD files but don’t seem to be able to find that information.

  2. Before I work to segment the MNI_avg152T1+tlrc atlas myself, I was wondering if there is an existing repository of extracted structures in MNI space (e.g., Left Amygdala, Right Putamen, etc. etc.) that lives somewhere in the AFNI directory or somewhere else that is open source but I can’t find?

Thank you so much!


Hi, Megan-

We distribute a lot of atlases—some are sets of ROIs, and others are probabilistic maps.

The probabilistic ones are typically left that way to both show the uncertainty with ROI delineation and allow the users to select their own values. Often, there is a sibling atlas created with firm ROI delineations that the distributing group made, so there is that option as well. (Indeed, in many cases one should probably think of atlases really as probabilistic anyways, due to heterogeneity of structures…) So, the answer to your first question would be that you, the user, can choose what threshold is most appropriate, based on your application, etc. If the question is to ask what threshold was used to make any accompanying atlas, then I think that might have to be resolved by testing different thresholds or reading the associated descriptive paper.

There is a lot of template+atlas information under this part of the AFNI documentation:
… and some links to various atlases/templaates here:

And Daniel Glen might write in here with extra information…


Adding onto Paul’s useful advice - the probabilistic atlases are generally not thresholded at all. The probabilities are typically a fractional overlap of some sort. The overlap is based on the template target for the multiple subjects and the alignment methods used to move all the subjects. The numbers actually used may be from 0-1, 0-100, 0-250, 0-79 for 79 subjects, …, almost anything the atlas developer thinks is appropriate. In AFNI, each sub-brick volume within the dataset contains the probability map for a particular region. and the subbrick label and atlas_points_list attribute in the header should reflect which region is associated with it.

These kinds of atlases are often simplified into a stricter definition for each region with a “maximum probability map” or MPM atlas. At each voxel, the region that has the largest overlap (the maximum probability) “wins” that voxel. We typically don’t look at the actual maximum probability, but the maximum probability is not necessarily a very large fraction. Typically, there is a minimum threshold like 5 or 10%, but that varies across atlases. The lower the threshold, the larger regions will tend to be where there is little overlap with neighboring regions.

In AFNI, there are a variety of probabilistic atlases available - the Desai atlases, the Eickhoff-Zilles cytoarchitectonic atlas, the Haskins Pediatric atlas, the Princeton Visual atlas, the Ventro-prefrontal Cortical atlas and the UNC infant atlases. These can also be made for surface analysis like the Princeton atlas. Those are included in the links Paul left and a little more specifically in these links:

Hi Paul, Thank you so much! This is very helpful.

Thank you so much, Daniel! I’ll look into those!