[Mne_analysis] MNE pca and SNR

Daniel G. Wakeman dgwakeman at gmail.com
Tue Nov 18 06:13:47 EST 2008
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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.


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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> Mne_analysis at nmr.mgh.harvard.edu
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