[Mne_analysis] MNE pca and SNR

Daniel Goldenholz daniel at nmr.mgh.harvard.edu
Tue Nov 18 07:19:30 EST 2008
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1. The snr issue is actually a very deep one. You are telling MNE how to set
up the regularization parameter, and yes, it will change the resulting
signals. The reason that happens is that there are many more brain states
than there are MEG sensor states. (this is that "ill-posed problem" thing).
As a result, we do a pragmatic thing, which is simplify the problem and make
it solvable - we add the constraint of minimizing the current at every point
in the brain (loosely described). But when we do that, we need to make a
somewhat arbitrary choice about how much weight to give that constraint.
Because there is no simply physical interpretation of what we are doing,
physiology cannot easily guide us here. In practice, I have no suggestion. I
defer to Matti.

2. I did some reading on the subject of artifact removal a few years ago. I
haven't kept up with the literature there. But I recall reading a relatively
compelling argument against using PCA for artifact removal that Dan hinted
at. Essentially PCA does not care if it also removes real brain data along
with artifact. One possible approach suggested out there was a related
technique, called ICA. I believe someone has written a matlab toolbox for
that. But the results there are still sometimes suspicious. If you trust
SSS, that may be an extremely powerful method to removal any artifact not
coming from the head. As for eye blinks and movements - you could consider
adaptive filtering. Another possibility is to fit several dipoles at the
anatomical location of the eyes, and fit data to them, and remove them. In
my playing around with these issues very briefly, I didn't find one perfect
solution. But many papers are out there saying they did.

Hope my vagaries are mildly useful

Daniel Goldenholz MD, PhD

On Tue, Nov 18, 2008 at 6:13 AM, Daniel G. Wakeman <dgwakeman at gmail.com>wrote:

>  Hi Marina,
> 1.  I think the lack of reply generally reflects people's tendency to leave
> it alone.  Please people chime in, if I'm wrong.
> 2.  There is no function in MNE that does a PCA.  The closest thing within
> MNE would be the ability of mne_browse_raw to create SSP projections.
>  However, I would not recommend using this for that purpose; again please
> chime in, if you disagree.  The next best possibility to work on this would
> be to use the excellent MATLAB toolbox to read the fif files into matlab
> remove the eyeblinks/cardiovascular artifacts using whatever technique you
> like best and save the data back and continue processing.  Just be very
> careful with your noise covariance matrices and your artifact extraction as
> many of these tools have dangerous consequences for the true brain data.
> Dan
> On 7 Nov 2008, at 13:39, Marina Papoutsi wrote:
> Dear MNE users,
> I have two questions that I hope someone can answer.
> 1) The first is about SNR. Following an older post that I made on SNR (left
> unaswered :-( ) I will attempt to rephrase the question, hoping to hear back
> from someone.
> I am still wondering about how to best use the option --snr in
> mne_make_movie. I have played around with the data a bit and changing the
> SNR value seems to make a difference in the stc files.
> So what is the best way to chose an SNR?
> a) use the default value (3) independent of whether this is reflected in
> your data
> b) estimate the mean SNR value (over the epoch time), which will be
> different for each subject and condition?
> At the moment, I have calculated the SNR for each subject and condition.
> The SNR value is between 1 and 2 and it is different for subjects and
> conditions. Will that be a problem when I need to do group-level statistics
> comparing different conditions?
> 2) The second question is about PCA. Is there any function in MNE that
> would allow one to do a PCA on the *.fif files to remove eye-blinks or
> cardiovascular related oscillations?
> Thank you in advance for the help,
> Marina
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