Convert Brainstorm FEM to Fieldtrip for EEG source modelling

MWB · November 4, 2020, 3:03pm

Hi everyone, first I want to thank all people involved in developing Brainstorm. This is a terrific software!

I build a FEM headmodel in Brainstorm from an individual MRI and electrode positions. Now, I would like to export the headmodel for further processing in fieldtrip.

I tried the out_fieldtrip_headmodel function, but did not succeed. Would anyone have an example script were the export is shown in detail?

Best regards,
Markus

tmedani · November 5, 2020, 12:18am

Hi @MWB

What do you mean by headmodel?
is it the FEM mesh model (in the anatomical side of brainstorm) or the computed leadfield (in the functional side of brainstorm)?

So, in both case, you can export your "headmodel" to matlab, by right click on the item, then File ==> export to matlab. You will have the data as they are stored in the Brainstorm database.
From this step, you need to adapt this data to Fieldtrip format.

As far as I know, the current Fieldtrip functions can not read the FEM mesh from Brainstorm,
but it's not difficult to adapt it.

Could you explain which headmodel you need? (FEM head mesh or the FEM LF)

Best
Takfarinas

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
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%

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Thanks