[Eeglablist] ICA analysis and Interpolation

[Andrea Helo]

Hi,

Thank you very much for your replies. They have been very useful. I will
follow the advice and I will interpolate after running ICA.

I have another question related to the filters this time.

I am filtering between 1 and 30 Hz before running ICA. I have read that
very low frequencies aren't good for ICA but the problem is that I have
also read that the amplitude of the components might be reduced when low
frequency are filtered.

D*o you thnik this might be a problem? In case it is *I have also found a
way to apply the ICA weights from 1Hz filtered data to the 0.1Hz filtered
data.

*Load 1Hz filtered data set after ICA has been conducted and bad
*>>>* components have been removed, then:*

*>>* TMP.icawinv = EEG.icawinv;
*>>>* *>>* TMP.icasphere = EEG.icasphere;
*>>>* *>>* TMP.icaweights = EEG.icaweights;
*>>>* *>>* TMP.icachansind = EEG.icachansind;
*>>>* *>>>>* % apply to epoched dataset
*>>>* *>>* clear EEG;
*>>>* *>>* EEG = pop_loadset('filename', [SUBJ{s}, '_bcgrem.set'],
'filepath', PATHIN);
*>>>* *>>* EEG.icawinv = TMP.icawinv;
*>>>* *>>* EEG.icasphere = TMP.icasphere;
*>>>* *>>* EEG.icaweights = TMP.icaweights;
*>>>* *>>* EEG.icachansind = TMP.icachansind;
*>>>* *>>* clear TMP;
*>>>* *>>* EEG = pop_saveset(EEG, 'filename',[SUBJ{s}, '_epoched.set'],
*>>>* *>>* 'filepath',PATHOUT);
*>>>* *>>* [ALLEEG, EEG, CURRENTSET] = eeg_store(ALLEEG, EEG, 0);
*>>>* *>>>>* end
*>>>* *>>* eeglab redraw;**



*Do you think this would solve the problem?* ... and I have another problem
related to the previous  point. I apply the same pre-processing (before
running ICA) to the two data sets (1Hz filtered data and 0.1Hz filtered,
following a protocol proposed by EEGLAB:
http://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline).  Using this
protocol I reject epochs automatically but I don't get the same number of
epochs in both datasets. The 0.1Hz filtered data is noisier, so I get less
good epochs and I can't pass the ICA components from one datasets to the
other. So, the questions are


*Should I just export the epochs from one dataset to the other?*



*Do you know how to do that?*

*THANK YOU IN ADVANCE FOR YOUR HELP!*

On Sun, Feb 28, 2016 at 1:39 AM, Tarik S Bel-Bahar <tarikbelbahar at gmail.com>
wrote:

> Hello Andrea, I think you are re-referencing at a good time.  If you
> haven't had a chance to, try Googling the eeglablist + your
> keywords/questions to find any similar posts from the past. Makoto's
> pipeline mentioned in past eeglablist posts has a
> prototypical data processing pipeline. Consider staying in ICA space
> and analyzing the components.
>
> You wrote: 1- Is it possible interpolate channel in epoched data or is
> it  better to always interpolate in continuous data?
> **Yes, I think either way is fine, but it may depend on the algorithm
> that is used for interpolation.
>
> You wrote: 2- I have removed bad channels to run ICA, so those
> channels are not in the list of channels to be interpolated anymore
> after ICA. So, is there a way to interpolate after removing channels?
> **Yes, u should be able to use the interpolate function in eeglab gui.
> See also the matlab help and Google online documentation on
> interpolation function in eeglab.
>
>
> **Let's say you have 2 infants. One has 45 good channels for ICA, and
> one has 40 channels for ICA. No problem. Each one has their own ICA. I
> assume you will then "remove the bad ICs" and "rebuild the EEG data"
> for each participant. Then you would interpolate channels for each
> participant. Then you would have ICA-cleaned data from two
> participants, with the same 64 channels for each participant.
>
> **Please note that various groups drop  low channels below the ears
> and eyes line before ICA for infant data, e.g., J. Richards)
>
> ***I would say take a look at the differences in any in ICA results
> when using jsut shorter (~1000 ms) epochs versus using longer (3000
> ms+) epochs. They shoud look very similar.
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> On Thu, Feb 25, 2016 at 8:39 AM, Andrea Helo <andreahelo at gmail.com> wrote:
> > Dear all,
> >
> > I have an issue regarding ICA for artifact correction that I really would
> > appreciate some help with. I would also  appreciate if someone could
> approve
> > or suggest any modifications in my pre-processing order.
> >
> > Here is some background information:
> > I have recorded children data (24-month-olds) with EGI, 128 channels.
> > The experiment contains 144 trials (72 per condition) where a picture is
> > presented during 500 ms  followed by a word (700 ms) then there is an
> > intertrial of 2500 ms (I trigger the trials manually when the child is
> > looking at the screen).
> > I exported the data, and I am currently starting to pre-process the data
> > using EGGLab.
> > I have created epochs of 3500 ms in order to run ICA to detect
> eye-movement
> > artifacts (I have chosen 3500ms because I would like to keep as much
> data as
> > possible for ICA. I would like to compare ERP in shorter epochs of 1000
> ms
> > later).
> >
> > My pre-processing order is the following:
> >
> > Filtering (1HZ-30Hz),
> > Reducing number of channels to 64 and then removing bad channels
> > Re-referencing to average
> > Epoching (3500ms),
> > Removing baseline,
> > Removing bad epochs
> > Running ICA to detect artifacts
> >
> > One thing I am not sure about is whether I am re-referencing- at the
> right
> > point.
> >
> > Another issue is interpolation. I have read that it is not recomended
> > interpolate before running ICA . So I am removing bad channels before
> > running ICA but as a consequence I am having different amount of channels
> > per subject. I have also read that it is possible interpolate after
> running
> > ICA but I am not sure how to do it and I have two doubts related to that:
> >
> > 1- Is it possible interpolate channel in epoched data or is it  better to
> > always interpolate in continuous data? I have run ICA in epoched data
> first
> > and after that I will have to interpolate in the epoched data.
> > 2- I have removed bad channels to run ICA, so those channels are not in
> the
> > list of channels to be interpolated anymore after ICA. So, is there a
> way to
> > interpolate after removing channels?
> >
> >
> > Thanks in advance for your help,
> >
> > --
> > Andrea
> >
> >
> > _______________________________________________
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>



-- 
Andrea
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