[Mne_analysis] mne_analyze inverse display problem

Jeff Eriksen eriksenj at ohsu.edu
Wed Jun 27 13:47:59 EDT 2012
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Alex,

I did mark the VREF channel as bad.

I used the --diagnoise switch so as not to have to worry about the
actually noise-cov matrix at this point.

The problem is not a scaling issue - it is a severe display issue/bug -
the entire pane goes completely white, no surface displayed, nothing, and
at that point I can not even get back to any of the three types of
inverses. The only way to continue is to exit mne_analyse and restart it.

Thanks,
-Jeff

On 6/26/12 11:50 PM, "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>
wrote:

>hi,
>
>> I tried ico-4 and ico-5, and still get the same results ­ poor
>>correlation
>> between scalp and cortical sources. I have not tried the ‹loose option
>>yet,
>> will do that this afternoon. I did try ‹diagnoise, and that seemed to
>> improve matters (though I do not know why ­ the manual says most users
>>never
>> need to use this), but I am experiencing issues with mne_analyse in
>>trying
>> to display the three different estimates.
>
>did you correct for the bad channel like matti suggested? did you take a
>look
>at the noise covariance you estimated from the data? Ideally it should be
>as diagonal as possible with similar values along the diagonal. See e.g.
>
>http://martinos.org/mne/auto_examples/plot_estimate_covariance_matrix_raw.
>html
>
>for an example of noise covariance plot.
>
>> As I change from dSPM, which comes
>> up as defult, to MNE, the inflated brain pane goes white, and I cannot
>>get
>> it back until I exit and go back in. Ever seen this before?
>
>you certainly need to adjust the scaling of the colorbar.
>
>do you see something like this:
>
>http://martinos.org/mne/_images/MNE_preferences.png
>
>taken from : 
>http://martinos.org/mne/manual/analyze.html#ch-interactive-analysis
>
>Alex
>
>
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