[Mne_analysis] Get back a reference channel from acticap

[Sylvain]

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Hello,


Thank you for your answer Clemens.

So in order to be clear in getting back FCz, referencing to average and then 
reducing dimensionality:

- first I add back FCz as a zeros channel;
- I compute the mean of each other channel and I substract 0 to this mean 
for FCz;
- I then compute the average reference (will be rank deficient);
- I use the function mne.preprocessing.ICA specifying that 
I want max_pca_components and n_pca_components to be equal to my number of 
channel minus 1.

Does it sound right?

Sorry for all the questions and thank so much for all these answers!

Sylvain

On Wed, 17 Oct 2018 09:37:59 +0000
  "Brunner, Clemens 
(clemens.brunner at uni-graz.at)"	<clemens.brunner at uni-graz.at> wrote:
>        External Email - Use Caution        
> 
> 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
> 
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