[Mne_analysis] misc concerns and questions with mne_analyze and 256-channel EEG data

[Alexandre Gramfort]

Hello Jeff,

you should use ico5 or oct6 for the source space. ico3 is too small.
you can try with a diagonal noise covariance if the topography do not
match the source estimates.

Alex

On Sat, Jun 9, 2012 at 8:34 PM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
> Dan, see my answers below,
> -Jeff
>
> On 6/8/12 7:33 PM, "Dan G Wakeman" <dgwakeman at gmail.com> wrote:
>
>>Hi see follow-ups in text
>>On 2012 Jun 8, at 20:08 , Jeff Eriksen wrote:
>>
>>> Hi MNE analyzers,
>>>
>>> I have just succeeded in manipulating my data so that I can use
>>>mne_analyze for interactive analysis. So far I have
>>>
>>> Exported EEG as EDF file
>>> Converted to FIF file
>>> Aligned electrodes to scalp surface
>>> Created a single event and averaged so I could treat my raw data as
>>>averaged data (only way to get to into mne_analyze, I am told)
>>> Created BEM, forward, and inverse
>>> Loaded all into mne_analyze
>>>
>>> Questions & concerns:
>>>
>>> Source solutions on inflated surface do not seem to bear any relation
>>>to the scalp EEG data plotted on the scalp surface
>>What does this mean? Could you explain with more detail? Possibly send a
>>screenshot? (though see below, it sounds like there may be some issues in
>>earlier stages, which would be better to send first)
> I have posted my files and some screenshots to DropBox:
> https://dl.dropbox.com/u/74096906/MNE/MNE_files.zip
> https://dl.dropbox.com/u/74096906/MNE/MNE_pix.zip
> For the time sample I have shown on the pictures, the sources should be
> concentrated in the frontal midline based on the scalp topography, but the
> sources on the inflated brain surface shows widespread activity with no
> obvious concentration in the fontal midline.
>
>>> I cannot get the MRI solutions to change as I change the time sample,
>>>thought the other displays behave appropriately
>>What do you mean by MRI solutions?
> I mean the source activity shown on the 3D MRI display - subject's own MRI
>
>>> Also, the single MRI solution looks like the dMNE ones, and does not
>>>change as I switch to MNE or sLORETA estimates
>>I'm not sure what you mean by "single MRI solutions" or "dMNE"? What
>>windows are you talking about please describe more details.
> I mean the color-coded activity shown in the 3D MRI display for a single
> time sample. By dMNE I actually meant the MNE estimate, one of three
> available to display, the other two being dSPM and sLORETA.
>
>>> I cannot figure out how to display any EEG on the right-hand Data
>>>window, even after choosing "Adjust/select trace layout/sample EEG"
>>Did you generate an EEG layout? See the manual ( mne_make_eeg_layout )
> I will look at that again. I assumed it would be able to find and use the
> set of layouts I made for the raw EEG.
>
>>> I can find no mention in the manual on how to adjust the display
>>>amplitude of the source waveforms in the bottom left pane
>>> MNE source locations are fairly evenly spread out across both
>>>hemispheres, but dSMP and sLORETA's are mainly confined to R hemi
>>> All the source waveforms appear to have DC shifts lasting for the
>>>entire epoch ­ this does not seem right
>>Well, if there are these long DC shifts there should be evidence in the
>>evoked data (or raw if this is raw data). Did you use baselines e.g. bmin
>>bmax? How clean are the averages? (maybe send a plot) How clean is your
>>noise covariance data (did you go through the raw data used to calculate
>>it).
> I did not truly average - I faked it out by setting a single event and an
> N of 1, so it would seem I had averaged - I was advised to do this so I
> could work in mne_analyze and have all the tools available to me that do
> not necessarily work for raw data
> There _should_ not be any baseline shifts in the raw/averaged data as I
> filtered 1-100 Hz, which should have removed the baseline globally for
> each channel - thus I did not use bmin/bmax
> I calculated the noise-covariance using the entire epoch
>
>>
>>
>>D
>>>
>>> All in all, I am not comfortable with what I am observing, and wonder
>>>if I have dome something grossly wrong in my analysis stream so far. I
>>>am post files and screenshots to DropBox if anyone is willing to assist
>>>me with any of the above.
>>>
>>> The best thing I can think of doing at this point is to create some
>>>simulated time courses and EEG and run it through the steps I have
>>>performed above.
>>>
>>> -Jeff Eriksen
>>>
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