[Mne_analysis] Best way to apply eye blink projections with the common average

[Marijn van Vliet]

Dear Matt,

in the MNE suite, EEG data *always* needs to have a reference set. If no 
reference is explicitly set, MNE will keep trying to add one (an average 
reference). This is currently not documented in the manual (I've created 
a ticket for this https://github.com/mne-tools/mne-python/issues/3538).

In your case, the default average reference is not desired, so you need 
to explicitly set a reference using the mne.io.set_eeg_reference() 
function. Doing this will cause MNE to stop adding the average reference 
all over the place. To explicitly tell MNE that the data has already 
been referenced, you would call mne.io.set_eeg_reference(raw, []). This 
will also remove any existing (inactive) average ref projections.

See the API documentation for more details:
http://martinos.org/mne/stable/generated/mne.io.set_eeg_reference.html

regards,
Marijn.


On 08/27/2016 11:34 PM, Boggess, Matthew Jozsef wrote:
> Hi Mainak,
>
> I had been explicitly removing the average projection as you 
> suggested, but it perplexingly still seemed to be getting applied. 
> After digging into the code, I think I found out why though. The 
> compute_proj_eog function seems to always add and apply an average 
> reference projection when making the eye blink epochs because the 
> epochs add_eeg_ref parameter is left at its default of True and is not 
> externally exposed (line 187 of ssp.py). Consequently, the 
> compute_proj_eog avg_ref parameter does not actually have any control 
> over whether the average reference gets applied. Is this correct? If 
> so, then perhaps this is a bug that needs to be fixed? Especially if 
> one wants to utilized EOG/ECG SSPs, but doesn't want to average 
> re-reference as Alex pointed out, but also if it is better to first 
> compute the projections and then re-reference. I personally was 
> interested in which order would be best as I am both re-referencing 
> and applying EOG projections.
>
> Thanks for getting back to me!
> Matt
> ------------------------------------------------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu 
> [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Mainak Jas 
> [mainakjas at gmail.com]
> *Sent:* Saturday, August 27, 2016 5:03 AM
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] Best way to apply eye blink projections 
> with the common average
>
> Hi Matt,
>
> You are indeed correct. Average reference will not only attenuate the 
> eye blink but may also spread it to other sensors. Therefore, it is 
> probably better to apply it after eye blinks have been removed. The 
> average reference is probably added by default while plotting the raw 
> data. Do you have the problem even when you remove the proj using 
> raw.del_proj() and turn off add_eeg_ref or avg_ref everywhere?
>
> Mainak
>
> On Wed, Aug 24, 2016 at 7:31 PM, Boggess, Matthew Jozsef 
> <MBOGGESS at mgh.harvard.edu <mailto:MBOGGESS at mgh.harvard.edu>> wrote:
>
>     Hello everyone,
>
>     By default, MNE seems to add an average reference projection to
>     the raw data. I then noticed that when computing an eye blink EOG
>     projection (using compute_proj_eog) the average reference
>     projection gets applied prior to the computation of the
>     projection. However, my intuition would be that you would not want
>     to apply the average reference projection first because it will
>     attenuate the eye blink artifacts and consequently make the
>     periods where you estimate the eye blink noise subspace relatively
>     less dominated by the eye blinks. Is there a recommended ordering
>     to computing and applying these projections?
>
>     Thanks in advance!
>     Matt
>
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