Atlas modifying for visualisation

[Keelin]

Hello,
I am trying to modify an atlas created in brainstorm for visualisation purposes.

My steps are:
From brainstorm, export the atlas to a matlab file.
Keeping same data structure, modify colours only.
Create new atlas in brainstorm, and import modified atlas from matlab.

The scouts load correctly, and I can see the new colours next to labels, but they do not appear on the brain image.
Is there a solution for this?
I am working with the latest version of brainstorm (April 29, 2024).
Thank you!!

[Raymundo.Cassani]

The Scouts do not appear on the 3D MRI slices, as the Scouts are surface scouts, they will be only displayed the cortex surface (where they were defined).

Please note that there is a difference between Anatomical parcellations (atlases in the MRI space) and Brainstorm atlases (sets of Scouts defined on source space grids, either surface or volume).

• Anatomical parcellations
  https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#Subcortical_regions:_Volume

• Brainstorm surface atlases:
  https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts

• Brainstorm volume atlases:
  https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_scouts

If working with volume source grids. It is possible to:

• Generate a Brainstorm volume atlas from the Anatomical parcellation
  https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

• Generate an MRI mask from Brainstorm volume Scouts:
  In the Scout tab > Scout > Export as MRI mask