[Eeglablist] Running ICA without the GUI

Bethel Osuagwu b.osuagwu.1 at research.gla.ac.uk
Wed Oct 23 08:31:11 PDT 2013


Hi Liad,
 A component is marked for removal if its corresponding value in EEG.reject.gcompreject is 1 (or perhaps nonezero).
This line removes any component marked for removal in EEG.reject.gcompreject:
EEG = pop_subcomp( EEG,[],0);

I usually just use the GUI to reject/mark the components for removal.
I am not sure why you do not want to use the GUI to visualize the components, but the line below can be used without the need for the main GUI to display the component so that you can mark them for rejection:
pop_selectcomps(EEG, [1 2] );%Displays components 1 and 2.

If you are interested in automatic artifact removal using ICA, you can find a few papers in the journals. There are also methods implemented in EEGLAB that you can look at:
http://sccn.ucsd.edu/wiki/Chapter_01:_Rejecting_Artifacts
http://sccn.ucsd.edu/pipermail/eeglablist/2012/005496.html

Bethel
________________________________________
From: liad.glz at gmail.com [liad.glz at gmail.com]
Sent: 23 October 2013 15:36
To: Bethel Osuagwu
Cc: eeglablist at sccn.ucsd.edu
Subject: Re: [Eeglablist] Running ICA without the GUI

Thank you Bethel. Did is what I already did. My questions refers to inspecting the components now, after saving the data set. Can i do it wothout a GUI? Should I just use topoplot, inspect the figures and rejects the bad components with another command? My question refers to the components inspection part - can that be done without the GUI?

Liad

Sent from my iPhone

On 21 באוק 2013, at 14:49, Bethel Osuagwu <b.osuagwu.1 at research.gla.ac.uk<mailto:b.osuagwu.1 at research.gla.ac.uk>> wrote:

Hi Liad
Run ICA from the GUI and when it finishes type EEG.history in the matlab's command prompt to see a line similar to this:
EEG = pop_runica(EEG, 'extended',1,'stop',1e-07,'interupt','on');
This is the line you will need to run the script outside the GUI.

Also make sure you save the dataset after the ICA. Once the dataset is saved, you should be able to move the dataset to another computer to continue processing the ICA.
The line to save the dataset outside the GUI looks like this:
EEG = pop_saveset( EEG, 'filename','EEG_ica.set','filepath','C:\myEEG');

I hope this helps.
Bethel

________________________________________
From: eeglablist-bounces at sccn.ucsd.edu<mailto:eeglablist-bounces at sccn.ucsd.edu> [eeglablist-bounces at sccn.ucsd.edu<mailto:eeglablist-bounces at sccn.ucsd.edu>] On Behalf Of liad glz [liad.glz at gmail.com<mailto:liad.glz at gmail.com>]
Sent: 20 October 2013 01:53
To: eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>
Subject: [Eeglablist] Running ICA without the GUI

Hello,

I want to first run the ICA on my computer, then save the output so I could inspect the components separately (on another computer), decide which ones to reject and run the rejection procedure. I know how it is done with the GUI, but I was not sure how to do it without it. I couldn't find in the Wiki what would be the function that would present the components so I could reject them after I run the runica.m, and what is the input this function would need, and the runica.m one generates? Are the weights enough, or do I need to save all the output components (weights,sphere,compvars,bias,signs,lrates,activations)?

Many thanks for your help
Liad




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