[Mne_analysis] Get back a reference channel from acticap

[Sylvain]

        External Email - Use Caution        

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:
>        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?
> 
> 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