[Mne_analysis] EEG reference for covariance matrices

Lucie Charles lucie.charles.ens at googlemail.com
Mon Apr 27 11:30:13 EDT 2009
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Hello !

I'm currently using the function mne_make_combined_event_file from the mne
matlab toolbox. This function gets the time of an event on a specified
channel and put it in a text file. But I've noticed that it doesn't get the
onset of the event but the offset of this event (the time when the channel
goes back to zero).
Why is that ? Is there any reason to look at the offset instead of the onset
?

Thanks in advance,

Lucie



2009/4/16 Matti Hamalainen <msh at nmr.mgh.harvard.edu>

>
> 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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