Exporting generated head models from and to matlab

wabood1 · December 4, 2020, 3:00pm

Hello,

Is it possible to used the electrode position file from brainstorm to compute the FEM source model using field trip in Matlab. I tried 'exporting' the electrode position to Matlab. I do see it as a variable but whenever I try to use it, I get an error. and If that is possible can I import the head source model to brainstorm so I can use it in 'computing source model' ?

Thank you

Francois · December 5, 2020, 8:07am

Note that Brainstorm now features DUNEuro, the successor of the SimBio toolbox (used in FieldTrip). Not fully documented yet, but soon.
https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro

The process Sources > FieldTrip: ft_prepare_leadfield would give you an example of how to convert Brainstorm structure into FieldTrip structures. Same for all the other process_ft_*.m functions.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_ft_prepare_leadfield.m

function varargout = process_ft_prepare_leadfield( varargin )
% PROCESS_FT_PREPARE_LEADFIELD: Call FieldTrip functions ft_prepare_headmodel and ft_prepare_leadfield.

% @=============================================================================
% 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.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@

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wabood1 · December 5, 2020, 1:48pm

THank you Francois, I treid your suggestion(ft_prepare_leadfield), with the following options:

Surfaces used for the head model
field trip: ft_volumesegment +........
Forward modeling method:
I tried all of the BEM options

I get the following error message

then I tried
surfaces : Brainstorm: surfaces from the database
->it finished successfully but as I was using ft_sourceanalysis I got another error message

Waleed

Francois · December 6, 2020, 7:52am

I never wrote the code to support FieldTrip FEM in Brainstorm, and calling the BEM has no interest since we have a direct support of OpenMEEG directly in Brainstorm.

What I had in mind was not to suggest that you use a Brainstorm process, but that you read the code of the process_ft_*.m functions for having examples of how to use the conversion to convert Brainstorm structures into FieldTrip structures (out_fieldtrip_*.m) and vice versa (in_..._fieldtrip.m).
Then read the FieldTrip-SimBio tutorials to learn how to compute a FEM solution in FieldTrip.

Is it for validation purposes that you want to use the FieldTrip FEM?

wabood1 · December 7, 2020, 2:54pm

I am just trying to find a way to generate a FEM head model from FEM mesh. I am successful in creating the mesh but DuNeuro is not working on any of the meshes generated regardless of the method I use. I am not sure if I am doing something wrong. I can view the mesh and it looks ok to me.

Francois · December 7, 2020, 4:08pm

Can you describe more precisely what "is not working" means?

Have you tried with very simple models? (source space downsampled to 50 vertices, FEM mesh generated with iso2mesh from BEM surfaces with very low resolution)

@tmedani

tmedani · December 7, 2020, 8:08pm

Hello all,

@wabood1 could try to reproduce the steps for a basic FEM head model as explained in this tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro#FEM%20head%20model

This will give you a general idea of how the process works.
Could you also share a screenshot of the errors that you have with DUNEuro.

You need also to check the position of the cortex and the electrodes with the mesh,
you can also read this part, https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewForward#EEG_within_brainstorm_template_.283_layers.29

Once you have this basic example working, you can use more complex models.

Let us know if you have further issues.

Best,