[Eeglablist] On ICA based artifact rejection
Stephen Politzer-Ahles
politzerahless at gmail.com
Thu Sep 6 10:24:22 PDT 2012
Hi Imali,
I don't have experience with using "reject based on ICA", but the first
option you pointed out (6A--using Tools>Reject components to remove the
IC(s) with artifact) works. What I have typically done is first use
Tools>Reject components to do that, and then use Tools>Reject epochs (by
inspection) on the cleaned data to go through and reject any epochs that
contain other artifact. (In my case, I use ICA to remove the blink
artifacts, but then must reject by inspection to remove artifact that's
left over such as skin potentials or EMG).
Maybe some others on the list can give you some more information about the
other methods, which I am not familiar with.
Best,
Steve
On Wed, Sep 5, 2012 at 10:28 PM, IMALI THANUJA HETTIARACHCHI <
ith at deakin.edu.au> wrote:
> Thank you very much Makoto, really appreciate your guidance and help.****
>
> ** **
>
> I have further some questions regarding ICA artifact rejection and
> localisation.****
>
> ** **
>
> In EEGLAb we use ICA for both artifact rejection and source localisation?
> As I want to use EEGLAB for my dipole localisation, I am a bit confused
> with the steps that I should follow, I read the details on artifact
> rejection given on the wiki and a thread on ‘Pipeline of processing to
> optimize ICA for artrifact removal’ on the discussion list, but still not
> clear on the steps. Below I will briefly give the steps which I understood
> that I should follow, can you please tell me whether my understanding is
> correct and comment if I have gone wrong somewhere?****
>
> ****
>
> **1. **Re-reference continues data (The data is collected on a
> bipolar montage so re-reference to the common average)****
>
> **2. **Reject unsuitable portions of data by visual inspection****
>
> **3. **High pass filter the data(cut-off @ 0.5Hz to preserve ERP
> components), low pass filter the data(cut-off 30Hz)****
>
> **4. **Extract epochs (without baseline removal???)****
>
> **5. **Run ICA****
>
> ** **
>
> Now I get confused, after the ICA decomposition I will be able to view the
> ICA components with *Tools> Reject data using ICA>Reject components by map
> *
>
> With this window I can detect the components for eye artifacts, muscle
> artifacts etc. Then is it,****
>
> ** **
>
> **6. ***A. Tools>Remove components *to subtract ICA components or
> should I do****
>
> *B.* *Tools> Reject data Epochs> reject data(all methods),(* but if I do
> this how can that be an artifact rejection* *by ICA)* *or ****
>
> *C.Tools>Reject data epochs>export marks to ICA reject *and then*Tools>Reject data epochs>Reject marked epochs
> *?****
>
> ** **
>
> Could you please make it clear to me how I should reject epochs using ICA
> after the first decomposition.****
>
> ***7. ***Then *Tools>Remove Baseline* and * Plot>Channel ERP’s *
> steps* *will give me the ERP for a particular stimulation?**
>
> ***8. ***Now to do dipole localisation Run ICA on the pruned data
> set and run DIPFIT, here won’t I get the same remaining ICA components from
> the first epoched data set?**
>
> ** **
>
> * *
>
> Many thanks,****
>
> Imali****
>
> * *
>
> ** **
>
> ** **
>
> ** **
>
> *From:* Makoto Miyakoshi [mailto:mmiyakoshi at ucsd.edu]
> *Sent:* Wednesday, 5 September 2012 7:02 AM
> *To:* IMALI THANUJA HETTIARACHCHI
> *Cc:* eeglablist at sccn.ucsd.edu
> *Subject:* Re: [Eeglablist] ERP localisation with BESA and DIPFIT with ICA
> ****
>
> ** **
>
> Dear Imali,****
>
> ** **
>
> ICA returns 'one map/IC per a component' which does not change across
> recording time.****
>
> A static location corresponds to a brain region.****
>
> If you think of averaged ERP topo, for example, scalp topography changes
> from timepoint to timepoint. Independent components are not like that.****
>
> ** **
>
> > 2. Do independent components for cognitive activity in brain
> represents ERP components(P1,N1, etc)?****
>
> ** **
>
> Not necessarily. One IC can explain 3 ERP peaks (P1/N1/P2 as one burst).**
> **
>
> ** **
>
> > 3. Since I have minimal(correct to say no..) experience in ERP,
> how do I know my dipole localisations with ICA are correct? For instance,
> in a visual task I would expect to see one or more dipoles in visual area,
> but when changing the conditions such as colour or shape where else do I
> get dipoles? Or simply, how do I have a hypothesis for the ICA component
> related dipoles?****
>
> ** **
>
> How do I know my dipole location is correct? ****
>
> When you calculate dipole fit, you'll have residual variance. If this
> value is small, that means your dipole location is good.****
>
> For symmetrical two dipoles, when the topography show bilateral pattern
> you should place two dipoles (This may require some prior knowledge about
> somatosensory mu, alpha, and EOG). ****
>
> ** **
>
> > 4. With very limited neuroscience knowledge how do I get around
> with localisations to extract a task related neuronal activity?****
>
> ** **
>
> If you don't have time to read Scott Makeig, Arnaud Delorme, or Julie
> Onton etc, then****
>
> 1. run ICA****
>
> 2. run dipfit (autofit)****
>
> Remember, 1 dipole for 1 (or bilateral 2) IC(s). They are always paired.
> ICA generates time-invariant scalp topo, and dipfit calculates the
> associated dipole(s) that is also time-invariant (ICs don't change their
> locations throughout your data just as your brain regions don't).****
>
> ** **
>
> If you have further questions please ask further.****
>
> ** **
>
> Makoto****
>
> ** **
>
> 2012/8/31 IMALI THANUJA HETTIARACHCHI <ith at deakin.edu.au>****
>
> Dear EEGLAB list,****
>
> ****
>
> While reading through papers for my experiments, I just became curious
> (with some confusion) on the dipole fitting approach of the ERP data(for a
> specific task). ****
>
> ****
>
> According to my understanding the ERP wave consists of several components
> such as P1,N1, P2 , N2 and P3 mainly (stimulus dependent). As I am
> intending to use ICA based source localization(using DIPFIT plugin) I
> wanted to find out on what degree the two dipole fitting approaches are
> differing in BESA and DIPFIT with ICA.****
>
> ****
>
> 1. Am I correct if I say that with BESA, dipoles can be fitted to
> individual components of the ERP waveform? ****
>
> 2. Do independent components for cognitive activity in brain
> represents ERP components(P1,N1, etc)? ****
>
> 3. Since I have minimal(correct to say no..) experience in ERP, how
> do I know my dipole localisations with ICA are correct? For instance, in a
> visual task I would expect to see one or more dipoles in visual area, but
> when changing the conditions such as colour or shape where else do I get
> dipoles? Or simply, how do I have a hypothesis for the ICA component
> related dipoles?****
>
> 4. With very limited neuroscience knowledge how do I get around
> with localisations to extract a task related neuronal activity? ****
>
> ****
>
> Sorry about throwing a lot of questions at the list, but I have always
> found EEGLAB list as very friendly and a very expertized group. So, your
> advice will be highly appreciated to move forward in my work.****
>
> ****
>
> Best regards****
>
> Imali****
>
> ****
>
> *Imali Thanuja Hettiarachchi*****
>
> PhD Candidate****
>
> Centre for Intelligent Systems research****
>
> Deakin University, Geelong 3217, Australia.****
>
> Email: ith at deakin.edu.au
> www.deakin.edu.au/cisr****
>
> ****
>
> [image: Description: Description: Description:
> cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD at deakin.edu.au]****
>
> ****
>
> ** **
>
> ****
>
>
> _______________________________________________
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>
>
> ****
>
> ** **
>
> --
> Makoto Miyakoshi
> JSPS Postdoctral Fellow for Research Abroad
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego****
>
> _______________________________________________
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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