[Mne_analysis] Get back a reference channel from acticap

[Brunner, Clemens (clemens.brunner@uni-graz.at)]

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Hi!


> Well I am saying exactly what you are saying:
> - data are acquired with FCz as the reference channel on the brainvision 
> system. I want to retrieve FCz;
> - so I was just about adding back FCz (zeros values), computing the average 
> reference (so the new FCz value will be zero minus the mean of other 
> channel);
> - then either staying with the average reference or switching to linked 
> mastoid.

OK, I must have misread your initial question. Yes, this approach looks perfectly fine.

Regarding the issue you encounter, this seems to be a bug. The problem seems to be order in which you perform setting the montage and setting/adding a reference channel. It looks like if you set the montage before you add a reference, this warning message is produced (and the location of the newly added reference channel is incorrect). If you do it the other way round (first adding the reference and then setting the montage), everything is OK. I'm pretty sure this is unintended behavior so I've opened an issue with an example using one of our example data sets: https://github.com/mne-tools/mne-python/issues/5619

Let's continue the discussion related to this behavior on GitHub.

Regarding the recording setup, we have a BioSemi system which uses a CMS and DRL electrode. I never fully understood how this works, but my intuition was that this electrode(s) serve(s) as a reference. So all other (normal) channels record voltages referenced to that reference electrode, which is not part of the recorded channels because it is by definition always zero. I'm pretty sure that this is not doing an average reference though.

What Stefan is saying is correct, but I disagree that there is a problem with adding back a reference channel. This is just a particular issue with ICA, which cannot deal with rank deficient data. Average referenced data is rank deficient, but this does not have anything to do with whether you added a reference channel or not before the average reference computation.

Whether or not you add back the (all zero) reference channel depends on what you want. If the reference channel happens to be in a location you're interested in, you need to add it back to the data before computing the average reference. If the reference channel is in a location you're not interested in anyways (e.g. on a mastoid), you don't need to add it to the data and you just compute the average reference using the electrodes you have. In either case, you end up with rank-deficient data, which might be problematic for ICA if you don't explicitly reduce the dimensionality by 1 beforehand.

Clemens