[Mne_analysis] Restore a reference electrode

[Lorenzo Alfine]

Dear Marijn,
thank you very much for your answer, it really clarified my ideas about
this issue.
I didn't apply any other reference before extracting the epochs so I guess
it's still Oz (even if I'm not able to see that channel). I will defenately
use the average reference!
Again, this really helped, thank you.

Lorenzo

On 6 January 2017 at 08:53, Marijn van Vliet <w.m.vanvliet at gmail.com> wrote:

> Dear Lorenzo
>
> EEG records voltage, which is the difference in electric potential between
> two points. The voltage between a reference electrode and itself is always
> zero. Interpolating this channel from the surrounding channels will give
> you approximately the same answer: the voltage at the reference electrode
> is zero.
>
> The mne.add_reference_channels function will add the reference channel for
> you set it to zero.
>
> This means that when you use channel Oz as a reference channel, you will
> not be able to clearly see occipital activity (activity in that region will
> translate to an inverse of this activity in the frontal regions). In this
> case it makes sense to transform to an average reference. With this
> reference, the voltage will reflect the difference in electric potential
> between each electrode and the mean of all electrodes. This is usually
> easier to interpret.
>
> A call to set_eeg_reference(ref_channels=None) should accomplish this.
> The error you get is related to MNE being hesitant to move from some custom
> reference to an average reference (this limitation has been removed in the
> development version of MNE). What kind of reference did you use when
> extracting the epochs? At any rate, you can disable the error message by
> manually setting epochs_clean.info[‘custom_ref_applied’] = False.
>
> Hope this helps!
>
> Marijn.
>
> --
> Marijn van Vliet
> w.m.vanvliet at gmail.com
>
>
>
>
>
> > On 5 Jan 2017, at 15:59, Lorenzo Alfine <lorenzo.alfine at gmail.com>
> wrote:
> >
> > Dear mne users,
> >
> > we're recording EEG with a 64 electrodes cap, using Oz as reference.
> > The final data are in brainvision format and when I call raw.info, the
> list chs has 64 items:
> > 63 EEG and 1 STIM.
> > For further analysis reasons (topomaps etc.) I would like to reconstruct
> the Oz channel,
> > so to have 64 EEG channels.
> >
> > My idea was to use, after epoching:
> >
> > mne.add_reference_channels(epochs_clean, 'Oz', copy=False)
> > epochs_clean.info['bads'] = ['Oz']
> > epochs_clean.interpolate_bads()
> >
> > Does it make any sense or am I missing some fundamental theoretical
> issue?
> > (For example interpolating could introduce some redundant information).
> >
> > Later I want to calculate an evoked object, so I thought about
> re-referencing to average:
> >
> > epochs_clean.set_eeg_reference(ref_channels=None)
> >
> > but I get this error:
> > Cannot add an average EEG reference projection since a custom reference
> has been applied to the data earlier.
> >
> > So I thought to bypass the error using add_channels() but I believe that
> this is not really what I'm looking for.
> >
> > Thank you in advance for any help,
> >
> >  LA
> >
> > MSc student, University of Padova
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170109/2772de6f/attachment.html