[Eeglablist] marking bad channels and interpolating at different stages of preprocessing & ICA

[Tarik S Bel-Bahar]

Hello Raquel,

1. To interpolate channels you would load up one file that has only
the good channels,
then load up a second file that has the full channel list,
and then run the channel interpolation function from
the eeglab gui. There are two or three options there which let you
tell eeglab where the full channel list is.
Go to Tools > Interpolate Channels. There are multiple
self-explanatory options there, I tend to use "all channels from other
dataset" that is loaded too.

2. After you average reference, you should be able to decrease the
rank of the ICA solution by either setting the PCA flag to chans-1 or
removing one of your current channels. I assume you're not including
the "externals" into ICA nor treating them as normal channels.

2b. Best to google past discussions of rank on past eeglablist posts
by experts, and also on makoto's pipeline. No, as far as I understand,
after fixing rank by either the pca flag or by removing a channel,
 if you were to remove yet another single 1 channel, you would not
have to reduce rank, because the total number of channels would be
reduced by 1 appropriately already when you drop that additional
channel.
I believe it's mainly/only for the "reduction in rank after average
referencing"  that matters for needing to adjust by chan-1.


see  The eeg_interp function and it's documentation. It's available
from the eeglab gui.
https://sccn.ucsd.edu/svn/software/eeglab/functions/popfunc/eeg_interp.m


see also easily googlable eeglablist discussions below
an example search in google is "eeglablist interpolate bad channels
site:sccn.ucsd.edu"

https://sccn.ucsd.edu/pipermail/eeglablist/2007/001945.html
https://sccn.ucsd.edu/pipermail/eeglablist/2006/001222.html
https://sccn.ucsd.edu/pipermail/eeglablist/2011/003944.html
https://sccn.ucsd.edu/pipermail/eeglablist/2011/004465.html









On Wed, Sep 7, 2016 at 1:41 PM, Raquel London
<raquel at dragondelapatagonia.com> wrote:
>
> Hi all,
>
> I have a few questions about how to handle bad channels & ICA in eeglab.
>
> 1.-
> I want to mark channels as bad, and thereby exclude them from the average reference first. Then run ICA, remove components, and only then interpolate the removed channel(s). Does this make sense?
> In eeglab, once I remove a channel with edit > select data > channel range (remove), I cannot find a way to interpolate it anymore. Is there a way around this issue?
>
> 2.A
> I have 64 channels + 4 externals, so I compute the average reference over the 64 channels.
> Because I have an average reference, the rank of the data goes down by 1, so I use EEG = pop_runica(EEG , 'extended',1,'interupt','on','pca',67);
> to reduce the number of ICs to match the rank. Is this right?
>
> 2.B
> Now, if I eliminate, say, 1 channel, I would have to reduce the rank by one more, right? But, what if I did interpolate before running the ICA, I would still have to reduce the number of IC's to 66, is that correct?
>
> Thanks so much in advance for your comments!
>
> Raquel
>
>
>
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to eeglablist-unsubscribe at sccn.ucsd.edu
> For digest mode, send an email with the subject "set digest mime" to eeglablist-request at sccn.ucsd.edu