[Mne_analysis] Get back a reference channel from acticap

[Sylvain]

        External Email - Use Caution        

Hey Philip,


Sadly I have a system with the reference being plugged with an external 
strand and located on FCz.
I have trouble understanding the difference between an "internal" reference 
and FCz itself. I do not know but to me it seems that at the end the voltage 
recorded at every electrode is just the difference with FCz. What is the 
difference with it being internal?

I really prefer the way it is working with Biosemi since CMS is not located 
on a position of the standard1020. Anyway I disgress but just for maybe 
further acquisition do you think it would be ok if I just plug the REF (so 
the FCz electrode supposedly) to a mastoid (since I wont use the mastoid for 
any analysis).

I know it is not directly linked to MNE so please apologize if I disgress.

Sylvain

On Wed, 17 Oct 2018 11:21:57 +0200
  Phillip Alday <phillip.alday at mpi.nl> wrote:
>        External Email - Use Caution        
> 
> 
> On 10/17/2018 09:16 AM, Brunner, Clemens 
>(clemens.brunner at uni-graz.at)
> wrote:
>>         External Email - Use Caution        
>> 
>> Hi Sylvain!
>> 
>> Can you upload your file to your Dropbox or Google Drive and share 
>>the link?
>> 
>> In general, your approach makes sense to me, but I don't really 
>>understand why your Brainamp has an average reference electrode. This 
>>doesn't make sense, because an average reference is by definition the 
>>average of all involved channels, which means you cannot have a 
>>dedicated electrode for this. Maybe the data are collected with a FCz 
>>reference, and then they are re-referenced to average afterwards?
> 
> This is exactly what happens on the actichamp system. Depending on 
>your
> cap layout and hardware revision, FCz is either a "normal" electrode 
>or
> a blue reference electrode that is in a separate cable strand like 
>the
> ground electrode is. You can see this when you're setting up the cap 
>and
> doing impedance measurements -- all of your impedances will be 
>really
> horrible until you set up FCz.
> 
> As Stefan hypothesized later, FCz is then left out after the 
>internal
> reference is applied (their terminology, see
> https://www.brainproducts.com/productdetails.php?id=42&tab=2 ; but I
> suspect that it's essentially an average reference or an approximate 
>way
> of doing the reference at infinity like in REST) so that the data 
>are
> full rank and "reference free".
> 
> (I really, really hate that term -- I think some BioSemi systems use 
>it
> to, but their physical reference electrode is labeled "CMS" for
> "common-mode sensor".)
> 
> Phillip
> 
>> 
>> Anyway, I think the actual file would help us track down your issue.
>> 
>> Clemens
>> 
>> 
>>> On 16.10.2018, at 16:58, Sylvain <madec at uni-potsdam.de> wrote:
>>>
>>>        External Email - Use Caution        
>>>
>>> Ok here is the code for replicating the error:
>>>
>>>
>>> import mne
>>> import pandas as pd
>>> import numpy as np
>>> from mayavi import mlab
>>> %matplotlib inline
>>> %gui qt
>>>
>>>
>>> # Open EEG file
>>> data_path = '/home/sylvain/Desktop/Participant01'
>>> raw_fname = data_path + '/Participant01.vhdr'
>>>
>>> ## Error further in the code (when adding reference channel) if I 
>>>open the 
>>> file this way
>>> #raw_file = mne.io.read_raw_brainvision(raw_fname,
>>> #                                  event_id={"actiCAP Data On": 
>>>9999},
>>> #                                  montage = 'standard_1020',
>>> #                                  preload=True)
>>>
>>> # The error diseapear if i just use this
>>> raw_file = mne.io.read_raw_brainvision(raw_fname,
>>>                                   event_id={"actiCAP Data On": 
>>>9999},
>>>                                   preload=True)
>>>
>>>
>>> raw_file = mne.io.add_reference_channels(raw_file, ['FCz'])
>>>
>>> raw_file.set_montage('standard_1020')
>>> raw_file.plot_sensors()
>>>
>>>
>>> Do you know where I could stock the file it is quite big?
>>>
>>> Thank you
>>>
>>> Sylvain
>>>
>>> On Tue, 16 Oct 2018 16:50:41 +0200
>>>  Alexandre Gramfort <alexandre.gramfort at inria.fr> wrote:
>>>>       External Email - Use Caution        
>>>>
>>>> please share a file and code snippet so we better understand the 
>>>> issue
>>>> and we can document it and eventually help people not having this 
>>>> problem again.
>>>>
>>>> if you have an issue, it's very likely someone else will have it 
>>>> too.
>>>>
>>>> Alex
>>>>
>>>> _______________________________________________
>>>> Mne_analysis mailing list
>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> 
>> 
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> 
> 
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis