I am trying to generate a head model from the default anatomy using OpenMEEG.
I have followed the BEM with OpenMEEG tutorial and obtained the head model.
However I would like an anatomical label (e.g. left precentral gyrus...) corresponding to each of the locations in GridLoc, which I understand contains all the possible source locations (vertices) coordinates in the leadfield.
I am guessing that the GridAtlas variable in the head model is meant to be filled with this information, but this variable seems to be empty even after trying to add some atlas from the Anatomy UI.
Could I have some hints on what steps I am missing to achieve this? Thank you.
I am guessing that the GridAtlas variable in the head model is meant to be filled with this information
No, GridAtlas stores the definition of the anatomical structures used in the case of mixed head models. If it is empty, it means you used either a surface head model or a volume head model.
All the data structures are documented in the introduction tutorials (if you haven't read them yet, it might save you a lot of exploration time to start by following them):
https://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel#On_the_hard_drive
However I would like an anatomical label (e.g. left precentral gyrus...) corresponding to each of the locations in GridLoc
For surface head models, this is available in the Atlas/Scouts fields of the cortex surface. Please read this introduction tutorial until the end and get back to us if you still have questions.
https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts
PS: I removed the reference to OpenMEEG in the title, since this is not related with the type of forward solution you use, it only depends on the subject anatomy.
Thank you for pointing me in the right direction. I found what I was looking for.
Just to confirm, I noticed that for most of the included atlases, the number of vertices are different from the total number of vertices in the cortex surface (15002). I assume this is simply because some vertices are not defined by the atlas. So this shouldn't matter when I'm corresponding a certain brain region to a list of vertices right?
The FreeSurfer surfaces are artificially closed, they include a large section that does not correspond to any anatomical structure (display only one hemisphere to see what I describe). These regions are not included in the anatomical atlases.