[Mne_analysis] questions regarding noise-cov matrix (NVM)

[Jeff Eriksen]

One more question: My data is 250 seconds long, and I am using the entire recording to calculate the NCM. Should I use only a portion?
-Jeff

From: Jeff Eriksen <eriksenj at ohsu.edu<mailto:eriksenj at ohsu.edu>>
To: "mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>" <mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>>
Subject: [Mne_analysis] questions regarding noise-cov matrix (NVM)

I have been having some difficulties with the inverse results from my 256-channelEEG, some of which may stem from my noise-covariance matrix, and have come up with the following questions:

For MEG, the manual suggests recording some MEG without a subject in the loop – room noise, basically. It also suggests for epilepsy work to use a segment of MEG (or EEG) that has no epileptiform activity. I am doing continuous EEG, with no discrete events to speak of, so I wonder if I should do a subject-less recording and use that as the basis of my noise-cov matrix. I would do that by applying the electrode Net to a styrofoam head covered with a saline soaked towel.

What is the use of the noise-cov supposed to accomplish in practical terms?

It has been suggested that I try the —diagnoise switch if my inverse results are not matching my scalp topography (they are not, to my eye). I did that, and it seems to have helped a bit, but why? Why does the manual say that most users should never need to use this option?

I would like to read the NCM matrix into Matlab to examine it, but I cannot understand the MNE Matlab routines (mne- and fif-) that allow me to do that – too many undefined terms. Can someone give me an explicit set of instructions of how to look at the NCM in Matlab?

Can I avoid the use of the NCM altogether, or set it to a diagonal identity matrix?

Thanks
--Jeff

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