[Eeglablist] line command for runica to select channels

Tarik S Bel-Bahar tarikbelbahar at gmail.com
Tue Apr 16 21:58:06 PDT 2019


Hi Cathy, quick notes below, all the best.

The help for eeglab functions is googlable, and one can also open
pop_runica or help pop_runica in the command line, as with most/all matlab
functions. According to the help below you probably want 'chanind', and
integer or cell array of channel indices (open EEG.chanlocs if you haven't)
to keep things simpler, one could remove those channels before ICA. Note
that one can always review the help and code for the actual eeglab function
(e.g. runica) instead of the wrapper function (e.g. pop_runica),.

% pop_runica() - Run an ICA decomposition of an EEG dataset using runica(),
%                binica(), or another ICA or other linear decomposition.
% Usage:
%   >> OUT_EEG = pop_runica( EEG ); % pops-up a data entry window
%   >> OUT_EEG = pop_runica( EEG, 'key', 'val' ); % no pop_up
%
% Graphic interface:
%   "ICA algorithm to use" - [edit box] The ICA algorithm to use for
%                 ICA decomposition. Command line equivalent: 'icatype'
%   "Commandline options" - [edit box] Command line options to forward
%                 to the ICA algorithm. Command line equivalent: 'options'
% Inputs:
%   EEG         - input EEG dataset or array of datasets
%
% Optional inputs:
%   'icatype'   - ['runica'|'binica'|'jader'|'fastica'] ICA algorithm
%                 to use for the ICA decomposition. The nature of any
%                 differences in the results of these algorithms have
%                 not been well characterized. {default: binica(), if
%                 found, else runica()}
%   'dataset'   - [integer array] dataset index or indices.
%   'chanind'   - [integer array or cell array] subset of channel indices
%                 for running the ICA decomposition. Alternatively, you may
%                 also enter channel types here in a cell array.
%   'concatenate' - ['on'|'off'] 'on' concatenate all input datasets
%                 (assuming there are several). 'off' run ICA independently
%                 on each dataset. Default is 'off'.
%   'concatcond'  - ['on'|'off'] 'on' concatenate conditions for input
datasets
%                 of the same sessions and the same subject. Default is
'off'.
%   'reorder'   - ['on'|'off'] re-order components by variance if that's not
%                 already the case. Default is 'on'.
%   'key','val' - ICA algorithm options (see ICA routine help messages).

On Mon, Apr 15, 2019 at 5:47 PM Reed, Cathy <Cathy.Reed at claremontmckenna.edu>
wrote:

> Hi,
> I want to run runica on a subset of channels.  I can select these channels
> via the gui but when I use the history command to get the line command, the
> runica line command does not include the channel selection.  It is unclear
> to me from the help whether I need to put in something like 'channels',
> 1:28 in the command line or what.
>
> Thanks, Cathy Reed
>
> -----------------------------------
> Catherine L. Reed, Ph.D.
> Dept of Psychology, Claremont McKenna College
> Email: cathy.reed at cmc.edu<mailto:cathy.reed at cmc.edu>
>
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