[Mne_analysis] Get back a reference channel from acticap

[Sylvain]

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Hello Stefan,


I somewhat get your idea but isn't rank deficiency occurring anyway when one 
use average reference? Since all electrode are becoming a linear combination 
of all the other one?
I mean I get your point but I am not sure if it is linked to the fact of 
adding back a reference.

Thanks,

Sylvain

On Wed, 17 Oct 2018 10:43:35 +0200
  Stefan Appelhoff <stefan.appelhoff at mailbox.org> wrote:
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> 
> Dear Sylvain, Clemens, and Alex,
> 
> regarding the rationale:
> 
> - Say you recorded from 10 electrodes and referenced against another 
> electrode
> 
> - You thus have 11 electrodes, one of which contains a "zero" signal 
> (the reference)
> 
> - If you now apply the average reference, you are reducing the 
>"rank" of 
> the data by one (see: 
> https://sccn.ucsd.edu/wiki/Linear_Representations_and_Basis_Vectors#EEG_Data_Reference_and_Re-referencing)
> 
> - Usually, the reference electrode is not included in the 
>re-referenced 
> data ... so then you will have 10 electrodes and "full rank" data
> 
> - The problem arises by including the 11th electrode, because then 
>you 
> would have rank deficient data.
> 
> - If you then re-reference the rank-deficient, average-re-referenced 
> data to mastoids again, you might run into problems (e.g., when 
>trying 
> to run ICA).
> 
> 
> I am not entirely sure about my reasoning, so another opinion would 
>be 
> appreciated.
> 
> 
> Best,
> 
> Stefan
> 
> 
> On 17.10.18 10:16, Sylvain wrote:
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>>
>> Hello Clemens!
>>
>>
>> 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.
>>
>> Now apart from the issues I had with various functions depicted in 
>>my
>> previous mail I am not 100% sure my rationale is ok.
>>
>> Now concerning a file here is one (it is compressed) so maybe you 
>>can see
>> what I was refering to with functions causing issues.
>> https://www.dropbox.com/s/9rnf5o391vbxwr6/File_EEG.rar?dl=0
>>
>> Thanks!
>>
>> Sylvain
>>
>>
>> On Wed, 17 Oct 2018 07:16:15 +0000
>>    "Brunner, Clemens
>> (clemens.brunner at uni-graz.at)"	<clemens.brunner at uni-graz.at> wrote:
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>>>
>>> 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?
>>>
>>> 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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