[Mne_analysis] Get back a reference channel from acticap

Phillip Alday phillip.alday at mpi.nl
Wed Oct 17 05:21:57 EDT 2018
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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
>>>
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>>
>>
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