what do you mean "loop on the scouts" for the atlas? I see ROI and the vertices attached to each ROI, how do i copy these vertices and paste them correctly into the atlas labeling variable (4495,1)?
Something like:
npmat.atlases.labeling = zeros(4495,1);
for i=1:length(bstmat.Scouts)
npmat.atlases.labeling(bstmat.Scouts(i).Vertices) = label_index;
end
(you'll need some coding skills with Matlab and a good understanding of all these structures in order to do this)
Is it the sulci map (15335x1)double that i am to copy and paste into the labeling(4495,1) variable of the collins head model?
I'm sorry, I have no idea where your surfaces came from. You will most likely need to use the Brainstorm cortex surface instead of the one that you have in you neuropype head model.
Also, where or how would i compute CSF?
These are labels on the cortex surface. There is no CSF.