[Mne_analysis] EEG reference for covariance matrices

[Matti Hamalainen]

Hi Elisabeth,

On Apr 16, 2009, at 12:33 PM, Elisabeth Fonteneau wrote:

>  Dear all,
>
> We have a question regarding the computation of covariance matrices  
> with EEG and MEG in MNE:
>
> The inverse is always computed on the average reference data (for  
> EEG).
> Therefore the covariance matrices should be computed on the average  
> reference too. Although the inverse solution, theoretically, does  
> not depend on the choice of reference electrode, one has to make  
> sure that the leadfield, covariance matrix, and data are referenced  
> in the same way when performing the computations in MNE. Apparently,  
> MNE always uses average reference for the leadfield and the data,  
> but not necessarily for the covariance matrices.
> This means that we have to use the option --projon when we are  
> computing the covariance matrices with mne_process_raw.
> If we use the --projoff option, then the covariance matrices are  
> computed with the acquisition reference, and therefore, the inverse  
> solution will be incorrect.
>
> Are we right?

You are bringing up an important point. However, this is automatically  
accounted for in MNE.

The average reference is equivalent to a projection operator. When the  
inverse operator is put together, this projection is automatically  
applied to the noise covariance matrix as well. Therefore, it is OK to  
leave the projection off when the noise covariance matrix is computed.

Incidentally, I have found that sometimes the (for reasons I do not  
exactly know) the EEG noise covariance is not as "good" when you look  
at its eigenvalue spectra as the MEG one. Therefore, especially when  
computing combined MEG/EEG estimates I usually regularize the noise  
covariance using --megreg 0.1 and --eegreg 0.1 options to  
mne_do_inverse_operator.

I hope this helps,
Matti




-------------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Building 149, 13th Street, Mailcode 149-2301
Charlestown, MA 02129-2060
USA

e-mail          msh at nmr.mgh.harvard.edu
Tel             +1 617 726 0323
FAX             +1 617 726 7422



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