[Eeglablist] runing ICA excluding some channels

[Arnaud Delorme]

The latest version of EEGLAB also allow you to choose the indices (or 
type) of the channels on which to run ICA (in the "Run ICA" menu). I 
agree with Johannes though that you might want to include EOG channels 
in the ICA decomposition.

Best,

Arno

Sarnthein Johannes wrote:
> Dear Maro,
> 
> 1) I am wondering why you would exclude EOG channels before running ICA for artefact rejection. I use them as my best markers for EOG artefacts, so I include them in the ICA-run for artefact rejection.
> 
> 2) We also record EMG on the arm. This has to be excluded before running ICA for artefact rejection. The script below gives an outline, how I run ICA on head channels only and append the arm channel in the end.
> 
> Best,
> Johannes
> 
> 
> %% uses EEGLAB scripts and suptitle.m, which is available at Matlab central
> %%
> [ALLEEG EEG CURRENTSET ALLCOM] = eeglab;
> EEG = pop_loadcnt(filename);
> [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
> eeglab redraw
> pop_eegplot( EEG, 1, 0, 1); 
> pause % do visual artefact marking and rejection now
> %%
> [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,  'setname', [subj.name{is},'_',condition]);
> EEG = pop_saveset( EEG, [subj.name{is},'_',condition,'.set'],'');
> [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
> visualmarked=CURRENTSET;
> eeglab redraw;
> 
> %% delete all sets except for visualmarked
> x=1:10;x(find(x==visualmarked))=[];
> ALLEEG = pop_delset( ALLEEG, x );
> eeglab redraw;
> 
> %% select channels for runica
> limb=[62]; %exclude 62(limb r) & 61(if VEOG == limb left) before ICA
> EEG = pop_select( EEG, 'channel',limb);
> [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET, ...
>     'setname', 'emg','save',[subj.name{is},'_',condition,'emg.set']);
> emg=EEG.data; % create emg variable to append in the end
> EEG = eeg_retrieve(ALLEEG, visualmarked); CURRENTSET = visualmarked;
> EEG = pop_select( EEG, 'nochannel',limb);
> [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET, 'setname', 'nolimb');
> eeglab redraw;
> 
> %% runica
> EEG = pop_runica(EEG, 'icatype','runica');
> [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
> % plot scrolled components
> pop_eegplot( EEG, 0, 1, 1);
> suptitle([subj.name{is},'_',condition,'.set'])
> print % prints components automatically!!!
> 
> %% plot spectra to detect artefact components
> figure; pop_spectopo(EEG, 0, [0  EEG.xmax*1000], 'EEG' , 'freq', [2.5], 'plotchan', 0, 'percent', 100, ...
>     'icacomps', [1:size(EEG.icaweights,1)], 'nicamaps',10, 'freqrange',[2 25],'electrodes','off');
> figure; pop_spectopo(EEG, 0, [0  EEG.xmax*1000], 'EEG' , 'freq', [20], 'plotchan', 0, 'percent', 100, ...
>     'icacomps', [1:size(EEG.icaweights,1)], 'nicamaps',10, 'freqrange',[2 25],'electrodes','off');
> 
> %% subcomp reject artefact components
> components= [5 11 47 58	1  6 7 22 23 24 40 48];
> EEG = pop_subcomp( EEG, components, 1);
> [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
> eeglab redraw;
> 
> %% saveset
> [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,  'setname', [subj.name{is},'_',condition,'ICA']);
> EEG = pop_saveset( EEG, [subj.name{is},'_',condition,'ICA.set'], ['']);
> [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
> eeglab redraw;
> pop_eegplot( EEG, 1, 0, 1);
> % change to edit figure
> suptitle([subj.name{is},'_',condition,'ICA.set'])
> %print
> icacleaned=CURRENTSET;
> 
> %% append emg
> EEG = eeg_retrieve(ALLEEG, icacleaned); CURRENTSET = icacleaned; % includes HEOG
> EEG.data=[EEG.data; emg]; % append emg variable created above to nolimb, which was ICAcleaned
> EEG.nbchan=EEG.nbchan+size(emg,1);
> EEG.chanlocs=pop_chanedit(EEG.chanlocs,  'load',{ 'fms63limb1.loc', 'filetype',''});
> [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,...
>     'setname', [subj.name{is},'_',condition,'ICAemg'],...
>     'save', [subj.name{is},'_',condition,'ICAemg.set']);
> eeglab redraw;
> pop_eegplot( EEG, 1, 0, 1);
> suptitle([subj.name{is},'_',condition,'ICAemg.set'])
> % now print out channel data plot
> 
> 
> -----Ursprüngliche Nachricht-----
> Von: eeglablist-bounces at sccn.ucsd.edu [mailto:eeglablist-bounces at sccn.ucsd.edu] Im Auftrag von Maro Machizawa
> Gesendet: Mittwoch, 23. Mai 2007 18:54
> An: eeglablist at sccn.ucsd.edu
> Betreff: [Eeglablist] runing ICA excluding some channels
> 
> Dear Colleagues,
> 
> First, I would like to run ICA (extended one) excluding a couple of channels, which are EOG bipolar channels. Because I would like to keep those channels in the same data set, I wonder if it is possible.
> 
> Secondary, if it is possible, I also need to remove some of artifactual ICs without affecting those EOG channels that were excluded from previous ICA.
> 
> If it is possible, an example of command scripts would be great help.
> 
> Best regards,
> Maro
> 
> 
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