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Forward problem solver

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Alejandro Ojeda edited this page Feb 5, 2019 · 2 revisions

pop_forwardModel

Use this function to:

  • Coregister the sensor positions in the EEG structure with a template.
  • Compute the lead field matrix.

The function first tries to look-up the channel labels of your montage in a precomputed head model template based on the Colin27 MRI. If the search is successful, the function returns immediately with the lead field that corresponds to your montage. If only a few channels match, it uses them to automatically estimate a warping from your channel space to the space of the skin layer of the template. If no match is found, the co-registration gui pops up and you need to continue the process manually.

Syntax:

EEG = pop_forwardModel(EEG, templatefile, conductivity, orientation);

Input arguments:

  • EEG: EEGLAB's structure with nonempty EEG.chanlocs structure.
  • templatefile: file path to the template head model on disk.
  • conductivity: conductivity of each layer of tissue, scalp, skull, brain. The default value is: [0.33, 0.022, 0.33] in S/m units, which is based on this paper.
  • orientation: if true, computes the orientation-free lead field, otherwise it constrain the dipoles to be normal to the cortical surface.

Output: EEG: EEGLAB's structure where EEG.etc.src.hmfile points to the saved head model file (usually located next to the .set file) containing the computed forward model.

This function may or may not pop up a GUI depending on whether the co-registration process is needed. Learn more about co-registration here.

Examples

Compute the forward model using default parameters

EEG = pop_forwardModel(EEG);

Same as above but explititely specifying the parameters

templatefile = headModel.getDefaultTemplateFilename();
conductivity = [0.33, 0.022, 0.33];
orientation = false;
EEG = pop_forwardModel(EEG, templatefile, conductivity, orientation);

Visualize the individualized head model

hm = headModel.loadFromFile(EEG.etc.src.hmfile);
plot(hm);

Note that in the example above, hm.plot also works because hm is a headModel object that defines its own plot function.

Check that there are not polarity issues (if there are, simply multiply the lead field matrix by -1 and save it)

hm = headModel.loadFromFile(EEG.etc.src.hmfile);
% Simulate an activation in a given ROI, here we use the left precentral gyrus
ind = hm.indices4Structure('precentral L'); % Find the indices of some ROI
x = zeros(size(hm.K,2),1);                  % Initialize a source vector  
x(ind) = 1;                                 % Set to 1 only the dipoles in the selected ROI   
% Simulate a scalp projection
y = hm.K*x;
% Plot simulations to make sure that both the cortical and scalp maps display activations in red
hm.plotOnModel( x, y);

% If the scalp activation is displayed in blue it means that the lead field has the polarity inverted, 
% this can happen on some surfaces. The issue can be easily fixed as follows:
hm.K = -hm.K;
hm.saveToFile(EEG.etc.src.hmfile);
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