Brainnetome atlas in default anatomy

Hi everyone, I need a suggestion. I'm trying to import brainnetome atlas in the brainstorm default anatomy surface with 15002 vertices but I think I'm doing something wrong. This is what I did:
I downloaded the .annot brainnetome label and surface, in the folder I found the two hemispheres separate.
I imported the surface of each hemisphere separately, importing the atlas label for each hemisphere.
Then, I merged the two hemispheres obtaining a surface with 123000 vertices with the complete brainnetome atlas. I downsampled the surface to 15002 and the I exported from brainstorm the .mat atlas.
I tried to import the brainstorm exported .mat atlas in the default anatomy surface, although even if I did not receive an error message when I plot the surface I obtain several colored dots on the surface instead of the atlas.
I'm sure that it is not correct to import an atlas obtained from a surface to another, but considering that brainnetome atlas is available on the freesurfer surface, what could I do to import it also on the brainstorm default anatomy?

There is no easy solution for this. The surfaces created by FreeSurfer are not exchangeable between subjects, the vertices do not match point-to-point between surfaces, they may even have different numbers of vertices. Therefore it is not possible to use the .annot files (= a texture that associates each vertex of a surface to a label) computed on one subject for another subject.

Do you have access to a full FreeSurfer folder (including T1.mgz, ASEG*.mgz, lh.pial, etc.) for the Braintome atlas?
We could import this into Brainstorm and make it a new template.

Yes I do. If you want I could share it with you and/or Martin. Let me know.

Yes please. You could zip the entire FreeSurfer folder, upload it anywhere and post the download link here.

This is the link:!QkBG2AjI!MnZTo0BB6HrFo02A3jPsmjp3o3GKE0BhW6j0JSIFEJA

Let me know if you have any problem in downloading the folder

Thanks for the files.

I realized that this is a parcellation scheme that you can project to any subject you process with FreeSurfer, following the instructions in the Brainnetome Atlas in Freesurfer and Workbench.

I've just added the instructions to load the *h.BN_Atlas.annot atlases when importing the FreeSurfer anatomy. Now whenever these files are available in the FreeSurfer folder "label", they'll be imported automatically by Brainstorm.


  1. Update Brainstorm
  2. Project the Braintomme atlas to your subject folder:
  3. Import the FreeSurfer folder:
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That sounds awesome! Does it mean that in case I use the default anatomy if I want to use the atlas I just need to use FSaverage instead of the ICBM 152, right?

I've just uploaded a new version of the FSAverage atlas, which includes the Brainetomme atlas:

To get it: update Brainstorm again, then right-click on an subject folder in the anatomy view > Use template > Download: FSAverage_2020.

If you have the MRI of your subjects, you should rather run FreeSurfer and project the Braintomme atlas on their own cortical surfaces.