[FieldTrip] Decreased baseline level after using ICA in ERP data

[Beom Jun Min]

Dear Diego,

Thank you for your kind answer.
The importance of 'quality' you mentioned and the references that you
attached could help me to understand the ICA algorithm further.
And I have an additional question about preprocessing before ICA. Is
detrending needed before the decomposition if there is a linear trend in
the segmented data?
Because I noticed one component showing linearly and consistently decreased
(or increased) activity during one segment in some trials after ICA, I
wondered why that happened.

Apart from that, I found the possible cause of the past problem. It looks
like the ft_rejectcomponent might remove the 'demean' effect.
After I used the function without any component removing, (cfg.component =
[];) the baseline level decreased again but the shape of the ERP does not
change.
However, I have not found the way to correct this decreased baseline yet.
The ft_preprocessing with demean pre-stimulus does not work.

Thanks.

BJ



2013/6/24 Lozano Soldevilla, D. (Diego) <d.lozanosoldevilla at fcdonders.ru.nl>

> Dear Beom Jun,
>
> I see multiple scenarios why this baseline activity decrease could happen.
> First of all, how the component you're rejecting look like (i.e. "blink
> component")? Do you see this activity decrease after the baseline period?
>
> The "quality" of the ICA decomposition, how well your artifact/component
> of interest has been isolated by algorithm in time (i.e. blink time
> courses) and space (marked frontal topography), will determine the activity
> that later on you'll reject/select. If your decomposition is not well
> suited, the rejection of a particular IC activity might have "extra"
> activity you don't want to reject (effect of interest), might be the
> algorithm is not able to isolate the components of interests (i.e.
> artifacts) or a combination of both.
>
> To evaluate the quality of your ICA decomposition you might have a look
> here (http://www.ncbi.nlm.nih.gov/pubmed/19162199). Basically, the
> authors find that the ICA decomposition improves significantly "increased
> by removing the mean EEG at each channel for each epoch of data rather than
> the mean EEG in a prestimulus baseline". In addition (see here:
> http://sccn.ucsd.edu/pipermail/eeglablist/2012/004925.html), high-pass
> filtering above ~1hz improve the results.
>
> It's very important to feed ICA as much relevant data as you can use. The
> more the data, the better the decomposition. There's a rule of thumb that
> says that for a reliable IC decomposition 20 time points per channel2  is
> needed (see here for a reference
> http://www.ncbi.nlm.nih.gov/pubmed/16904745)
>
> I hope that helps,
>
> Diego
> ------------------------------
>
> *From: *"Beom Jun Min" <mbj0310 at gmail.com>
> *To: *"FieldTrip discussion list" <fieldtrip at science.ru.nl>
> *Sent: *Monday, 24 June, 2013 6:27:47 AM
> *Subject: *[FieldTrip] Decreased baseline level after using ICA in ERP
> data
>
>
> Dear all,
>
> I have ERP data and now I am dealing with ICA to remove muscle and eye
> artifacts.
> However, I found that after ft_rejectcomponent, the baseline level of the
> segmented epoch decreased. (The baselinewindow is [-0.2 0].)
> The baseline level decreased even though I rejected only one component.
>
> My script is shown below.
>
> *%% Removing the Artifacts*
> *cfg = [];
> *
> *cfg.component = [ ]; % to be removed component(s)*
> *post_ICA_temp6 = ft_rejectcomponent(cfg, comp_detrand, data_raw);*
> *
> *
> *%% timelocking*
> *
> *
> *cfg = [];*
> *timelock_temp6 = ft_timelockanalysis(cfg, post_ICA_temp6);*
> *
> *
> *%% Plot*
> *
> *
> *figure;*
> *cfg = [];*
> *cfg.layout = lay;*
> *cfg.interactive = 'yes';*
> *cfg.channel = ['all', {'-EKG', '-EMG'}];*
> *ft_multiplotER(cfg, timelock_temp6)*
>
> Is there something that I missed?
>
> Thanks.
>
> BJ
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> --
> PhD Student
> Neuronal Oscillations Group
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> NL-6525 EN Nijmegen
> The Netherlands
> http://www.ru.nl/people/donders/lozano-soldevilla-d/
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130625/f3ac3e63/attachment-0002.html>