[Eeglablist] re referencing to average after ICA

[Raquel London]

Hi Tarik and everyone,

As promised, I thought I'd share the steps I took that resulted in much
better decompositions. I tested some of these steps together due to time
constraints, so I can't be exactly sure how much of the improvement is due
to which step. I know that greatly reduces the usefulness of my post, but I
thought I'd just share it anyway. Thanks for all the help I got with this
on the list.

What I ended up doing
- Set the eeglab preferences to double precision
- High pass filter at 0.5 Hz (I know you recommend 1 Hz, but I used .5
because I found it to be much more common in the literature about my
topic). Compared to the .1 Hz filter I used before, this was already a huge
improvement.

For ICA I used short epochs so no components would be wasted on artifacts
outside the time window of interest. Later, I applied these weights to the
dataset that was epoched with buffer zones to accomodate edge artifacts for
TF analysis.

- Epoch to the time window of interest (no buffer zone) and do linear
baseline correction to the mean of the whole epoch. (see
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062525/)
- Get rid of any super bad channels (if the noise on the channel was such
that I thought ICA might pick it up, I left it in for now)
- Average reference
- Super thorough artifact rejection, throwing away even slightly weird
trials I would normally keep.
- Run ICA; I reduced the number of components that eeglab returns like this
(I had 68 channels): EEG = pop_runica(EEG , 'extended',1,'interupt','on','
*pca',67*);

Here I went back to the continuous, high-pass filtered data

- Epoch to the time window of interest plus buffer zones and do linear
baseline correction to the mean of the whole epoch.
- Average reference
- Apply the ICA weights to this file, do component rejection
- If there were any very bad channels that ICA couldn't clean, I'd go all
the way back to before ICA and get rid of the channel and redo everything
for this subject
- Trial rejection
- Laplacian

cheers,
Raquel

On Sat, Sep 3, 2016 at 10:24 PM, Tarik S Bel-Bahar <tarikbelbahar at gmail.com>
wrote:

> Thanks for your question Raquel, and great idea to get a better idea of
> the mechanics and assumptions. Hands-on playing with different options and
> rerunning ICAs can be quite useful. What I meant is that usually
> researchers, as far as I understand, usually apply the ICA decomposition to
> files (from processing steps before ICA) that are very similar to the files
> that went "into" ICA. But there are various ways the files could be the
> "same"....
>
> In other words, the usual thing is to apply the ICA weights to a file that
> has at least
> ***A. the *same* channels as the file(s) that went into ICA
> ***B. the *same* subject and same recording session as the file(s) that
> went into ICA
> I think this is due the basic expectations of ICA and the data structures
> in eeglab.  Also, each person/session of course has their own decomposition.
>
>
> FURTHER
> ***C. Usually,the file which is getting the ICA weights will be the *same
> *as the file(s) that went into the ICA (e.g, in terms of filtering or
> bandpassing or re-referencing). Relatedly, I don't believe it's appropriate
> to apply ICA weights from 1hz-highpass files to unfiltered files, but I
> might be wrong.
>
>
> HOWEVER
> ***D. The file which is getting the ICA weights does not need to have the *same
> *exact time points as the file(s) that went into the ICA, and it can be
> epoched or continuous. As long as it has the correct features matching the
> file that went into ICA. So it's in terms of time points to apply the ICA
> weights to that you have the most freedom, relative to other feature of the
> data.
> Thus.... one can re-apply to the continuous or near-continous epoched
> data, and then do artifact rejection with ICA info, re-do epoching after
> doing ICA cleaning, and other similar strategies. Some of the strategies
> are laidout in the eeglab tutorials and articles.
>
>
> ps. when things are setup wrong with ICA, the solutions will look weird,
> the eeg data will look weird, and/or eeglab will break. If you get a chance
> to, please consider sharing some examples of your next tests, or some
> summary of your understanding that could benefit new users later on.
>
>
>
>
>
>
>
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