[Eeglablist] How to make an ICA run in less than a week?

[Baris Demiral]

Hi James,

1- For frequency of interest of 200Hz, you can down-sample your data
down to 512Hz. But before that, low-pass filter your data with cut off
value of 250Hz or so. Follow Nyquist theorem.
2- You can run ICA on continuous data, but make sure you have marked
AND rejected the bad segments in the EEG data, since bad recording
WILL influence your ICA analysis A LOT. Pre-processing is still
important, even though ICA will eventually be used to reject artifacts
later. SO, observe your data well.
3- Xeon processors should have more than 2 cores I think. Run parallel
MATLABs on the same computer over the different cores for different
sets of subjects.

Arno, and other eeglab gurus, do you have any plans to
implement/combine ICA routines with parallel computing toolbox in
matlab?  Is it possible to create, say, a PARICA? Is this
theoretically possible? For instance, ICA routine can divide the data
into 4 or so and then combine them over different cores/machines?

Cheers,
Baris

On Fri, Jul 13, 2012 at 1:07 PM, James Schaeffer <schaefj3 at gmail.com> wrote:
> Hi All,
>
>
> Thanks for your help.  I have started using binica and it is going a bit
> faster.  We have chosen to use a high sampling rate (2048 Hz) because we
> thought it might be needed for cross-frequency coupling analysis with high
> gamma up to 200 Hz.  If I downsample, will I still be able to see these
> relationships?
>
>
> Thanks again,
>
> James
>
>
> On Thu, Jul 5, 2012 at 6:24 PM, James Schaeffer <schaefj3 at gmail.com> wrote:
>>
>> Dear eeglablist,
>>
>> I am running ICAs on 10 minutes of Biosemi EEG data, collected from 128
>> channels, and sampled at 2048 Hz. However, the ICAs have been running for a
>> few days without much progress. Two computers have 8G RAM and an Intel(R)
>> Xeon(TM) CPU 2.80GHz. One has been running an ICA for 6 days and is on step
>> 33; the other, for 4 days, and is on step 28. Another computer has 12G RAM
>> and an Intel(R) Xeon(R) CPU 5110 @ 1.60GHz; it has been running for 3 days
>> and is on step 60. All are running openSUSE 12.1 (x86_64), with eeglab
>> version 10.2.2.4b. The 'free' command indicates that they are not using any
>> swap space.  Should it be taking this long?  Is it possible that we have
>> more than the one copy of the data in ram or that Matlab or Eeglab has
>> placed something else in ram, or is busy with other processes? Is there
>> anything I can do to speed up this process? Any help would be greatly
>> appreciated.
>>
>> Thanks in advance,
>> James
>
>
>
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-- 
Ş. Barış Demiral, PhD.
Department of Psychiatry
Washington University
School of Medicine
660 S. Euclid Avenue
Box 8134
Saint Louis, MO 63110
Phone: +1 (314) 747 1603