[Eeglablist] Using the 'command' field of eeg_plot to reject trials
Makoto Miyakoshi
mmiyakoshi at ucsd.edu
Mon Jun 30 11:49:10 PDT 2014
Very good to know, thanks!
Makoto
On Mon, Jun 30, 2014 at 11:23 AM, Mikołaj Magnuski <
imponderabilion at gmail.com> wrote:
> It depends on a number of things. For example some of the eeglab functions
> that you call may be declaring EEG as global or evaluating it in workspace
> (but in such case this should happen whatever name you gave to the variable
> passed as EEG).
> In some cases it may be safer to declare EEG as global / evalin yourself.
> I remember once having a function that kept working on the same file
> instead of looping through multiple files. The global declaration in one
> of the eeglab functions was overwriting the EEG that it got passed with the
> previously global EEG (the first EEG processed).
> To avoid these perils one can declare EEG as global at the relevant level,
> use evalin('base', 'EEG', EEG) or clearvars -global EEG :)
> 30 cze 2014 19:01 "Makoto Miyakoshi" <mmiyakoshi at ucsd.edu> napisał(a):
>
> Thanks MIkolaj. Actually I did not know it. It seems it has been
>> automatically taken care of in my case probably because I have launched
>> EEGLAB before using any of eeglab functions...
>>
>> Makoto
>>
>>
>> On Sat, Jun 28, 2014 at 12:15 AM, Mikołaj Magnuski <
>> imponderabilion at gmail.com> wrote:
>>
>>> Dear Matthew and Makoto,
>>>
>>> synchronizing with base workspace eeglab GUI usually requires a bit more
>>> (unless you want to change your function into a script).
>>> The easiest way is to declare relevant eeglab variables as globals at
>>> the beginning of the function (EEG, ALLEEG, etc. - whatever eeglab
>>> variables you are using and want to sync with workspace gui). For example:
>>> global EEG
>>>
>>> Unfortunately, using globals is usually frowned upon by programmers (for
>>> good reasons) but I don't think you should worry too much when using
>>> globals in small applications.
>>>
>>> Another way however would be to assign (see assignin docummentation)
>>> relevant eeglab variables in the base workspace and evaluate (see evalin)
>>> eeglab GUI commands in the base workspace too.
>>>
>>> Try globals first. EEGlab declares most (if not all) of the all-caps
>>> base workspace variables as globals and synchronizes the gui functions (at
>>> least some of them) with the workspace this way - so you should be fine
>>> with global variables (from my experience - using globals is the easiest
>>> and most efficient way of creating and synchronizing GUI data in matlab
>>> without blocking the command window with uiwait( ) etc. ).
>>> 28 cze 2014 05:35 "Makoto Miyakoshi" <mmiyakoshi at ucsd.edu> napisał(a):
>>>
>>> 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
>>>>
>>>> _______________________________________________
>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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>>>>
>>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>
--
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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