[Eeglablist] ICA at Script Level

Simon-Shlomo Poil simonshlomo.poil at cncr.vu.nl
Wed Oct 13 15:15:05 PDT 2010


Dear Edward,

Did you try just to set  EEG.icaweights, EEG.sphere?
i.e. run the first line of your script. Then check if you can plot the
activations.

hope that works.
-Simon

-- 
Simon-Shlomo Poil

Neuronal Oscillations and Cognition Group (NOC)
Department of Integrative Neurophysiology (INF)
Center for Neurogenomics and Cognitive Research (CNCR)
Neuroscience Campus Amsterdam
VU University Amsterdam
De Boelelaan 1085, Room B-435
1081 HV Amsterdam, The Netherlands

E-mail: simonshlomo.poil at cncr.vu.nl
Phone: +31 20 5989408
Webpage: http://www.poil.dk and http://www.cncr.nl

2010/10/12 Modestino, Edward J *HS <EJM9F at hscmail.mcc.virginia.edu>:
> Dear EEGLAB experts,
>
> If you have a background in EEGLAB scripting and can help me with this, I
> would greatly appreciate this.
>
>
>
> I have been referring to this, but not able to solve the problem:
> http://sccn.ucsd.edu/wiki/Chapter_02:_Writing_EEGLAB_Scripts
>
>
>
> Recently, I have had great trouble running ICA on my data using the GUI due
> to memory constraints.  We have not been able to fix this otherwise.  So, I
> have moved to the script level using a low memory script level version of
> ICA.  I load my dataset into the GUI and then run the script through the
> GUI.  Here is the script I have been using.
>
>
>> [EEG.icaweights EEG.sphere] = runicalowmem(reshape(EEG.data, EEG.nbchan,
> EEG.trials*EEG.pnt
s));
>
> EEG = eeg_checkset(EEG);
>
> [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG, CURRENTSET);
>
> eeglab redraw;
>
>
>
> Here is the command window output:
>
> “Input data size [62,1048575] = 62 channels, 1048575 frames
>
> Finding 62 ICA components using logistic ICA.
>
> Decomposing 272 frames per ICA weight ((3844)^2 = 1048575 weights, Initial
> learning rate will be 0.000157494, block size 70.
>
> Learning rate will be multiplied by 0.9 whenever angledelta >= 60 deg.
>
> More than 32 channels: default stopping weight change 1E-7
>
> Training will end when wchange < 1e-007 or after 512 steps.
>
> Online bias adjustment will be used.
>
> Removing mean of each channel ...
>
> Final training data range: -2048.65 to 1315.39
>
> Computing the sphering matrix...
>
> Starting weights are the identity matrix ...
>
> Sphering the data ...
>
> Beginning ICA training ...
>
> Warning: Using 'state' to set RAND's internal state causes RAND, RANDI, and
> RANDN
>
> to use legacy random number generators.
>
>> In runicalowmem at 896
>
>   In pop_runscript at 50
>
> step 1 - lrate 0.000157, wchange 5985964.09709237, angledelta  0.0 deg
>
> .
>
> .
>
> .
>
> step 127 - lrate 0.000000, wchange 0.00000008, angledelta 50.9 deg
>
> Sorting components in descending order of mean projected variance ...”
>
>
>
>
>
> It appears from the command window that ICA ran on the data.  However, the
> current loaded dataset that ICA was run on says there are no ICA weights
> (GUI attached).  When I go to plot components, it says ICA needs to be run
> first.  So, clearly it ran but did not save the ICA to the dataset.
>
>
>
> I thought that this following command would overwrite the variables in the
> workspace: [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG, CURRENTSET);
>
>
>
> I thought this following command would update the display in the GUI: eeglab
> redraw;
>
>
>
> However, this is not working.
>
>
>
> Please help me if you can.
>
> Thanks,
> Ed Modestino
>
>
>
> Edward Justin Modestino, Ph.D.
>
> Postdoctoral Research Associate
>
> Ray Westphal Neuroimaging Laboratory
>
> Division of Perceptual Studies
>
> Department of Psychiatry and Neurobehavioral Sciences
>
> University of Virginia
>
> Email: ejm9f at virginia.edu
>
>
>
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