[Eeglablist] Using the 'command' field of eeg_plot to reject trials

[Makoto Miyakoshi]

Dear Matthew,

Looks like you want to automate the epoch rejection process.

> My problem may be that I can't seem to find how to load the eeglab
workspace variables, other than through the gui.

I recommend you replace all eegData in your code to EEG for the sake of
simplicity. As long as they are 'EEG' by typing 'eeglab redraw' you can
interact with it through EEGLAB main GUI.

To load data, use EEG = pop_loadset()... of course you can do eegData =
pop_loadset()... but again using 'EEG' allows you to interact it via GUI.

Makoto


On Tue, Jun 24, 2014 at 9:44 PM, Matthew Moore <matthew.moore at otago.ac.nz>
wrote:

>  Hi,
>
> I am having a bit of trouble getting eegplot to allow inspection and
> editing of candidates for rejection.
>
> I have looked at this thread:
> http://sccn.ucsd.edu/pipermail/eeglablist/2011/004085.html
>
> I tried to implement the command listed there, but am having trouble. My
> problem may be that I can't seem to find how to load the eeglab workspace
> variables, other than through the gui.
>
> I would really appreciate if someone could have a look at the code and
> give me some pointers.
>
> Matt
>
> function cleanedEEGData = detectArtefacts(eegData,locFile)
> %DETECTARTEFACTS Detects artefactual data using EEGLAB's functions, then
> %   displays the data in a plot for the user to check.
> %   Returns the eegData with artefactual trials removed.
> %   locFile is the file containing electrode locations.
>
>     epochLength=eegData.xmax;
>     epochTimeFrames=eegData.pnts;
>     sampleRate=eegData.srate;
>     events=eegData.event;
>     nElec=eegData.nbchan;
>
>     %Absolute limit of electrode values in uV
>     lowerLimit=-150;
>     upperLimit=150;
>
>     %Maximum slope over an epoch in uV/epoch
>     maxSlope=60;
>     rVal=0.3;
>
>     %Reject unlikely epochs, by number of SDs
>     sdJPSingleChan=4;
>     sdJPAllChans=4;
>
>     %Reject abnormal distributions, by number of SDs
>     sdKurtSingleChan=4;
>     sdKurtAllChans=4;
>
>     %Reject abnormal spectra
>     thresholds=[-50 50;-100 25];
>     frequencies=[0 2;20 40];
>
>     %Do the error detecting.
>
> eegData=pop_eegthresh(eegData,1,1:nElec,lowerLimit,upperLimit,0,epochLength,1,0,0);
>
> eegData=pop_rejtrend(eegData,1,1:nElec,epochTimeFrames,maxSlope,rVal,1,0,0);
>
> eegData=pop_jointprob(eegData,1,1:nElec,sdJPSingleChan,sdJPAllChans,1,0);
>
> eegData=pop_rejkurt(eegData,1,1:nElec,sdKurtSingleChan,sdKurtAllChans,1,0);
> %     eegData=pop_rejspec( eegData,
> 1,'elecrange',1:30,'threshold',thresholds,'freqlimits',frequencies,'eegplotcom','','eegplotplotallrej',1,'eegplotreject',0,'specdata',eegData.specdata);
>
>     %Get the format for marking trials in an eegplot
>
> plotRejThr=trial2eegplot(eegData.reject.rejthresh,eegData.reject.rejthreshE,epochTimeFrames,eegData.reject.rejthreshcol);
>
> plotRejTre=trial2eegplot(eegData.reject.rejconst,eegData.reject.rejconstE,epochTimeFrames,eegData.reject.rejconstcol);
>     plotRejJp
> =trial2eegplot(eegData.reject.rejjp,eegData.reject.rejjpE,epochTimeFrames,eegData.reject.rejjpcol);
>
> plotRejKur=trial2eegplot(eegData.reject.rejkurt,eegData.reject.rejkurtE,epochTimeFrames,eegData.reject.rejkurtcol);
> %
> rejSpe=trial2eegplot(eegData.reject.rejfreq,eegData.reject.rejfreqE,epochTimeFrames,eegData.reject.rejfreqcol);
>
>     %Put the reject candidates in one array.
>     rejE=[plotRejThr;plotRejTre;plotRejJp;plotRejKur];%;rejSpe];
>
>     %command string for reject marked trials... all marked epochs...
>     %from http://sccn.ucsd.edu/pipermail/eeglablist/2011/004085.html
>     cmd = [ ...
>     '[tmprej tmprejE] = eegplot2trial( TMPREJ,EEG.pnts,EEG.trials);' ...
>     '[EEGTMP LASTCOM] = pop_rejepoch(EEG, tmprej, 1);' ...
>     'if ~isempty(LASTCOM),'...
>     ' [ALLEEG EEG CURRENTSET tmpcom] = pop_newset(ALLEEG, EEGTMP,
> CURRENTSET);' ...
>     ' if ~isempty(tmpcom),' ...
>     '  EEG = eegh(LASTCOM, EEG);' ...
>     '  eegh(tmpcom);' ...
>     '  eeglab(''redraw'');' ...
>     ' end;' ...
>     'end;' ...
>     'clear EEGTMP tmpcom;' ...
>     ] ;
>
>     %Draw the data.
>     eegplot(eegData.data,...
>         'eloc_file',locFile,...
>         'srate',sampleRate,...
>         'events',events,...
>         'winrej',rejE,...
>         'command',cmd,...
>         'butlabel','Reject');
>
>
> end
>
>
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-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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