[Eeglablist] ica cleaning: removing epochs or components?

[Makoto Miyakoshi]

Dear Jenny,

Sorry for slow response.

> But that seems like a "waste" to me since I would have to take out epochs
that are actually fine but where just one electrode is out of range.

I agree with you. If there are apparent artifacts, and you don't mind
manually removing them (when you have you have < 20-30 datasets) go ahead
remove them before first ICA.

> So I was wondering whether it would actually make sense to generously
remove all components that are associated with one crazy electrode at one
time point, and then run the ica again instead of deleting the whole epoch.

We take ICA-decomposed brain EEG as ground truth, so we don't bother to
clean the 'back-projected' scalp channel EEG signals. If you follow the
EEGLAB STUDY steps, those single-channel ICs will be cleaned automatically.
Check the whole preprocess pipeline, starting from the data import to the
group-level analysis, in the following link. You'll notice that how
creating STUDY can take care of most of artifacts.

http://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline

I also recommend you check clean_rawdata plugin.

Makoto



On Wed, Nov 5, 2014 at 2:43 AM, Jenny-Charlotte Baumeister <
baumeist at sissa.it> wrote:

> Hi everyone,
>
> I have a question regarding the cleaning after the ica. I cleaned my
> continuous data (by rejecting periods with movement artifacts after visual
> inspection), next I epoched the data and ran the ica on this (128 channels,
> 650 epochs of 1sec at 256Hz).  It turns out that I have several components
> that account for only one electrode in single epochs.
> I recorded from 128 electrodes and the experiment was very long so it
> seems natural to me that sometimes one electrode for a short time period
> shows improbable activity and goes back to normal after 1 epoch or so.
> Now I read that after the ica I should go on and clean the epochs but not
> yet remove any components.  I read that I should do so only after I ran the
> second ica on the pruned data. But that seems like a "waste" to me since I
> would have to take out epochs that are actually fine but where just one
> electrode is out of range. Also interpolating the affected electrodes over
> all trials doesn't seem like a good idea to me since most of the time the
> electrode shows abnormal activity only for a brief time window.
> So I was wondering whether it would actually make sense to generously
> remove all components that are associated with one crazy electrode at one
> time point, and then run the ica again instead of deleting the whole epoch.
> Alternatively, I was wondering about interpolating broken electrodes in
> specific epochs only - is that appropriate and if yes how can it be done?
>
> I would be very grateful for any suggestions and input on this!
>
> Thanks a lot in advance
> Jenny
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-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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