Freesurfer template aparc+aseg vs aseg atlas

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1

The default Brainstorm labelled aseg atlas (tess_aseg.mat) is a pleasure to use, however I need also the bilateral subcortical region "ventral DC" (region #28 in the screenshot under section 2 here)... Is it at all possible to have a version with it included? (In other words a tess_aparc+aseg.mat?)
Otherwise, is there some simple way to add it?
Grateful for any help!

2

You can load the APARC+ASEG.mgz volume as a volume atlas (Scout tab), or a set of surfaces (right-click on subject > Import surface).
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

4

Hi @Francois, thank you for your directions! Unfortunately I still haven't been able to generate the figure I wanted... (sorry if I'm being obtuse!)
What I do want is for the end figure to look like is this, created by following TutorialDba (using tess_aseg.mat) but including the "L &R ventral DC"

what_it%20_should_look_like_but_include_ventralDC
what_it%20_should_look_like_but_include_ventralDC1830×996 315 KB

Here is what I did (please tell me what I did wrong!) to import the aparc+aseg.mgz downloaded from Freesurfer:

  1. double clicked on "aseg atlas" under "Default anatomy". (Because otherwise the options within the "Scout" tab are not clickable...)
  2. Under "Scout" tab, chose "Load atlas" > aparc+aseg.mgz
    (which file format amongst "Volume mask or atlas [...]" should I choose? The one that kind of works that I've tried is [no overlap, MNI space].)
  3. It asks if I want to apply a standard transformation, so I say "Yes" and I get this:
    42
    42998×1424 196 KB

but it's not like the wanted well-defined structures as when following TutorialDba....

Please help! :sob:

5

Copy the mgz file somewhere else, rename it to remove the "aseg" word, so it is not interpreted as an ASEG atlas by Brainstorm.
Then Import surface > File format = Volume mask or atlas (subject space).
Downsample the resulting atlas before displaying it (it contains > 1 million vertices)
In the Scout tab, the atlas Structures contains the meshes.

It might be more meaningful to compute volume source models and import your atlas as ROIs

6

Thank you so much @Francois it worked!! :smile:

8

Hi @Francois , one further question: if I use tess_cortex_pial_low.mat as used in the TutorialDba, the subcortex doesn't go inside the "cortex" and I get an image as below -- how can I fix this?

35
351376×1424 241 KB

Thanks again, your help is much appreciated! :pray:

9

This might get complicated to figure out how all the changes of coordinates systems are working...
I think the easiest would be to load everything from the same FreeSurfer output. Do no try to use the default anatomy (MNI ICBM152 template) at all: load the FreeSurfer folder for your subject (menu Import anatomy folder) and then add the additional atlas you want (Import surfaces).

10

Thank you so much for your help @Francois !!! :smile: