[FieldTrip] ICA - Can I visualize Activity power spectrum of single components?

[KatrinH Heimann]

Diego, can I ask you another advice- this time more conceptually? I am
playing with the ICA now and experience, that I get very different
components depending on the artifact detection that I do beforehand. So my
idea (due to the literature) was, that the ICA works better on already
cleaned data. Now, as I want to do a frequency analysis afterwards, I did
not want to reject parts of trials. Therefore I deleted a relatively big
amount of trials in which I found muscle artifacts/drifts (Say 25% of the
whole amount of trials). However, in fact I see that the ICA then does not
give me easily to interpret components anymore - actually the results are
better (that is easier to interpret which is artifact, which not) if I
include all trials. If I only reject parts of the trials it gets even a bit
better. So my question is: Shell I a) do the (stricter) artifact detection
rather after the ICA or b) perform it on data with parts of trials marked
as bad - in which case I also ask: can I then still reject those components
in the uncleaned data (saved beforehand) so that I do not get problems with
the frequency analysis afterwards...?!
Thanks a lot for your help!!! Katrin


2014-05-28 15:02 GMT+02:00 KatrinH Heimann <katrinheimann at gmail.com>:

> Wonderfull! Thanks Diego!!!!
> Cheers k
>
>
> 2014-05-28 14:24 GMT+02:00 Lozano Soldevilla, D. (Diego) <
> d.lozanosoldevilla at fcdonders.ru.nl>:
>
> Hi Katrin,
>>
>> First, to display the independent components:
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> cfg = [];
>> cfg.layout = 'CTF151.lay'; % specify the layout file that should be used
>> for plotting
>> cfg.viewmode = 'component'
>> ft_databrowser(cfg, comp)
>>
>> Take a look to the following example script:
>>
>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts
>>
>> Second, you'll have to compute the power spectrum for each independent
>> component with ft_freqanalaysis:
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> cfg              = [];
>> cfg.output       = 'pow';
>> cfg.channel      = 'all';%compute the power spectrum in all ICs
>> cfg.method       = 'mtmfft';
>> cfg.taper        = 'hanning';
>> cfg.foi          = 2:2:30;
>> freq = ft_freqanalysis(cfg, comp);
>>
>> And you can plot the spectra:
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> nsubplots = 25;
>> nbyn = sqrt(nsubplots);% sqrt(nsubplots) should not contain decimals,
>> type doc subplot
>>
>> Nfigs = ceil(size(comp.topo,1)/nsubplots);
>> tot = Nfigs*nsubplots;
>>
>> rptvect = 1:size(comp.topo,1);
>> rptvect = padarray(rptvect, [0 tot-size(comp.topo,1)], 0,'post');
>> rptvect = reshape(rptvect,nsubplots,Nfigs)';
>>
>> for r=1:size(rptvect,1);
>>   figure;set(gcf,'units','normalized','outerposition',[0 0 1 1]);%full
>> screen
>>   k=0;
>>   for j=1:size(rptvect,2);
>>     if~(rptvect(r,j)==0);
>>       k=k+1;
>>       cfg=[];
>>       cfg.channel = rptvect(r,j);
>>       subplot(nbyn,nbyn,k);ft_singleplotER(cfg,freq);
>>     end
>>   end
>> end
>>
>> For the IC topos you'll follow the same logic as above but with:
>>
>> figure
>> cfg = [];
>> cfg.component = [1:20];       % specify the component(s) that should be
>> plotted
>> cfg.layout    = 'GSN-HydroCel-129.sfp';
>> cfg.comment   = 'no';
>> ft_topoplotIC(cfg, comp)
>>
>> I hope it helps
>>
>> Diego
>> ------------------------------
>>
>> *From: *"KatrinH Heimann" <katrinheimann at gmail.com>
>> *To: *"FieldTrip discussion list" <fieldtrip at science.ru.nl>
>> *Sent: *Wednesday, 28 May, 2014 12:59:38 PM
>> *Subject: *[FieldTrip] ICA - Can I visualize Activity power spectrum of
>> single        components?
>>
>>
>> Dear all,
>> another question:
>> Is it possible to visualize the Activity power spectrum of the single
>> components after an ICA by using ft_databrowser (or something else). I like
>> this feature from EEG lab as I find it easier to detect artifactual
>> components.
>> Thanks a lot for your help
>> Katrin
>>
>>
>> _______________________________________________
>> 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
>>
>
>
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