Computing the resolution matrix with loose orientations

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1

Hi all,

I’m new to the forum and hope I’m asking my question in a constructive manner :slight_smile:

I’m on MNE 0.20 (maybe that’s the problem, but this is inside a larger software development project and updating hasn’t been done yet) on Ubuntu 20.04.

I’m working with a high density EEG dataset with 18 subjects, head models derived from individual MRIs. I’m trying to implement the region growing algorithm described in this paper, and for that I need the resolution matrix.

I’m trying to use mne.minimum_norm.make_inverse_resolution_matrix. The inputs are the forward solution, which I compute with:

fwd = mne.make_forward_solution(
            info, trans=trans, src=src,bem=bem, meg=False, eeg=True, mindist=mindist, n_jobs=4)

which results in

<Forward | MEG channels: 0 | EEG channels: 128 | Source space: Surface with 8196 vertices | Source orientation: Free>

I compute the inverse operator with:

inverse_operator = mne.minimum_norm.make_inverse_operator(
			epochs.info, fwd, noise_cov, loose=1, depth=None, fixed=False)

So as you can see, I am trying to use free orientations with the intention to take the normal component later.

Within make_inverse_resolution_matrix, the function _get_matrix_from_inverse_operator is called, which returns the matrix that is necessary to obtain the resolution matrix by multiplying it with the leadfield. In the docstring of this function, it states “Currently works only for fixed/loose orientation constraints. For loose orientation constraint, the CTFs are computed for the normal component (pick_ori=‘normal’).”

The way I interpret this docstring is that if I used loose orientations, as I did, this function will pick the normal orientation, the result being a single magnitude. So I would expect a resolution matrix of size 8196 x 8196 (number of vertices). However, I get a resolution matrix of dimensions 24588 x 24588 which seems to indicate that the normal orientation was not picked, and I do not know how to handle 3D-CTFs here.

I have tried using an inverse operator with fixed orientations and converting the forward solution to 1D (using mne.forward.convert_forward_solution), but the resulting localization errors are enormous, so I would really like to stick to loose.

How can I get a resolution matrix with size 8196 x 8196 without fixing orientations?

Thanks for your help!
Best,
Katharina

2

apologies for the slow reply! Did you manage to solve the issue yourself? If not, maybe @olafhauk, @larsoner, or @agramfort might know the answer?

3

Hi! Thank you for replying :smile: I haven’t solved it :frowning: Help would indeed be appreciated. Maybe I’m just misunderstanding something.

4

This seems like an issue with either the documentation or the functionality. It does not seem like pick_ori='normal' actually gets used. I think it might actually be better if it doesn’t use the normal ori, and gives back something that has 3 entries for each location, along the lines of VectorSourceEstimate. @glombkat can you open a GitHub issue for this? We can figure out the right thing to do there.

5

Hello! Thank you!! I opened an issue ( #10187), hopefully correctly. Let me know if I need to edit it or add info.