Importing BEM model and electrodes in Brainstorm

Ottavia · March 10, 2023, 8:59am

Hello everyone,

I'm very new to Brainstorm and I would like to use this tool for the analysis of EEG data.
I already have an MRI individual scan for each participant (in ctf coordinates), the volume conduction model (I use a BEM in ctf coordinates) and a .mat file with the electrodes aligned to the BEM.
I tried to import these files in Brainstorm, but when I visualize the head model and the electrodes the latter looks not aligned with the scalp.

Can someone help me with this issue, please?
Do you confirm that Brainstorm can successfully read this files computed with other softwares? For the source model, the head model and the electrodes alignment I used Fieldtrip.

Thank you in advance for your help!

Cheers,
Ottavia

Francois · March 10, 2023, 12:21pm

Do you confirm that Brainstorm can successfully read this files computed with other softwares? For the source model, the head model and the electrodes alignment I used Fieldtrip.

I don't recommend you use a MRI converted to a .mat file with FieldTrip, as Brainstorm does not read the same information from the original volume.
I'm sorry, no easy solution exists for importing head model and source models from FieldTrip.

I recommend you import the original MRI from Brainstorm, and from there follow the pipelines described in the online tutorials.
https://neuroimage.usc.edu/brainstorm/Tutorials

If you want to manually import your previous FieldTrip results into your Brainstorm database, you need to be very comfortable with Matlab scripting, with the Brainstorm data structures and database, and probably also with 3D geometry programming (e.g. 4x4 transformation matrices). You can find some inspiration from the FieldTrip processes available in Brainstorm, like process_ft_volumesegment.m.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_ft_volumesegment.m#L258


      
              cfg = [];
              cfg.tissue = OPTIONS.layers;
              cfg.numvertices = OPTIONS.nVertices;
              ftMesh = ft_prepare_mesh(cfg, ftSegmented);
              if isempty(ftMesh)
                  errMsg = 'Something went wrong during the execution of the FieldTrip function ft_prepare_mesh. Check the command window...';
                  return;
              end
          end
          
          % ===== SAVE OUTPUT IN DATABASE =====
          sMriTissue = [];
          % Save each layer as a volume and a surface
          for i = 1:length(OPTIONS.layers)
              % If layer was not computed
              if ~isfield(ftSegmented, OPTIONS.layers{i}) || isempty(ftSegmented.(OPTIONS.layers{i}))
                  continue;
              end
              % Get layer name
              switch (OPTIONS.layers{i})
                  case 'white', bemName = 'white';       SurfaceType = 'Cortex';     iTissue = 1;