Convert Brainstorm FEM to Fieldtrip for EEG source modelling

Francois · November 5, 2020, 11:11am

The function out_fieldtrip_headmodel.m is supposed to convert a Brainstorm "headmodel.mat" structure to a FieldTrip leadfield structure.
However, DUNEuro (and FEM in general) is not supported yet.

What is missing in this function is an extra case 'duneuro', which creates a structure similar to what FieldTrip would generate for FEM foward modelling.
You are more than welcome to contribute to the improvement of this conversion function: when you have a prototype, please open a new PR on the Brainstorm github, and we will finish the integration from there.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_fieldtrip_headmodel.m#L121


    % Check if the surfaces are available
    if isempty(sSubject.iInnerSkull)
        error('No inner skull surface available for this subject.');
    else
        disp(['BST> ' HeadModelMethod ': Using the default inner skull surface available in the database.']);
    end
    % Load surfaces
    SurfaceFiles = {sSubject.Surface(sSubject.iInnerSkull).FileName};
    ftHeadmodel.bnd = out_fieldtrip_tess(SurfaceFiles);
    
case {'openmeeg', 'dipoli', 'bemcp'}
    ftHeadmodel.type = HeadModelMethod;
    % Check if the surfaces are available
    if isempty(sSubject.iInnerSkull) || isempty(sSubject.iOuterSkull) || isempty(sSubject.iScalp)
        error('No BEM surfaces available for this subject.');
    else
        disp(['BST> ' HeadModelMethod ': Using the default surfaces available in the database (inner skull, outer skull, scalp).']);
    end
    % Load surfaces
    SurfaceFiles = {sSubject.Surface(sSubject.iScalp).FileName, ...
                    sSubject.Surface(sSubject.iOuterSkull).FileName, ...

For converting the 3D tetrahedral mesh to a "FieldTrip headmodel", we need to modify the function out_fieldtrip_tess.m, which currently only supports surface triangulated tesselations.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/out_fieldtrip_tess.m

function ftSurf = out_fieldtrip_tess(SurfaceFiles)
% OUT_FIELDTRIP_TESS Converts multiple surfaces to an array of FieldTrip structures
% 
% USAGE:  ftSurf = out_fieldtrip_tess(SurfaceFiles)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
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Thanks