How do I run ICA only on certain channels using the code for pop_runica in Matlab eeglab?

Hi all,

I have an EEG.data matrix including 21 EEG channels (1:21, :), and 1 ECG channel (22, :).

I am trying to write a code to run pop_runica in eeglab, so I can run it from the Editor Window instead of using the GUI.

When using the GUI, I select Tools > Decompose data by ICA > runica and I select EEG as my channel types. This allow me to run ICA on EEG channels only (excluding my ECG channel).

However, this selection does not appear in the code when I call eegh, and I am unable to make this data selection when I use a code in the editor window. The 'chanid' specification from the pop_runica() function should allow to specify what channels I want to run the ICA on, but if I specify it, I get the following error: " Output argument "sphere" (and maybe others) not assigned during call to "runica". Error in pop_runica (line 439) [EEG.icaweights,EEG.icasphere] = runica( tmpdata, 'lrate', 0.001, g.options{:} ); Error in SSS_preprocess (line 99) EEG = pop_runica(EEG, 'icatype', 'runica', 'extended',1, 'interrupt', 'on', 'chanid', EEG.data((1:21), :), 'pca', EEG.eegrank);

I am using the following code:

%% 2. Run ICA

[EEG ALLEEG CURRENTSET] = eeg_retrieve(ALLEEG,1);

EEG = eeg_checkset( EEG );

EEG.eegrank = EEG.nbchan - size(EEG.etc.noiseDetection.interpolatedChannelNumbers, 2) - 2; % Nbchan minus interpolated channels, reference channel, and ECG.

EEG = pop_runica(EEG, 'icatype', 'runica', 'extended',1, 'interrupt', 'on', 'chanid', EEG.data(1:21, :), 'pca', EEG.eegrank);

[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);

Please would you be able to help? What should I specify after 'chanid' to select only my EEG data for ICA?

Many thanks in advance!!

Irene

Answer 1

[Vatsal]

Hi Irene,

The ‘chanid’ parameter in the “pop_runica” function is used to specify the channels on which you want to run the ICA. The ‘chanid’ parameter should be a vector of channel indices, not the actual EEG data. So, if you want to run ICA on the first 21 channels, you should pass a vector from 1 to 21 to ‘chanid’.

Here is how you can modify your code:

%% 2. Run ICA
[EEG, ALLEEG, CURRENTSET] = eeg_retrieve(ALLEEG, 1);
EEG = eeg_checkset(EEG);

EEG.eegrank = EEG.nbchan - size(EEG.etc.noiseDetection.interpolatedChannelNumbers, 2) - 2; 

% Specify the channel indices for EEG channels only (1 to 21)
chanidx = 1:21;

% Run ICA on the specified EEG channels
EEG = pop_runica(EEG, 'icatype', 'runica', 'extended', 1, 'interrupt', 'on', 'chanind', chanidx, 'pca', EEG.eegrank);

[ALLEEG, EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);

Please note that I have corrected 'chanid' to 'chanind', which is the appropriate argument for specifying channel indices in the “pop_runica” function.

To learn more about “pop_runica” usage and syntax, you may refer to the link below: -

https://github.com/sccn/eeglab/issues/430

https://github.com/sccn/nemar_tool_proof_of_concept/blob/master/pop_runica.m

I hope this helps!