James - <div><br></div><div>AMICA (Jason Palmer) runs in parallel on a cluster (Linux, Windows, Mac OS). It is also the most powerful ICA for EEG (Delorme et al., PLoS One, 2012) and the ICA algorithm we use by default now at SCCN (though extended infomax ICA in EEGLAB as runica() and binica() is related and 2nd most powerful of the ~22 linear blind source separation algorithms we compared).</div>
<div><br></div><div>Scott<br><br><div class="gmail_quote">On Wed, Jul 25, 2012 at 12:41 PM, James Desjardins <span dir="ltr"><<a href="mailto:jdesjardins@brocku.ca" target="_blank">jdesjardins@brocku.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF">
<div>Hi Baris,<br>
<span></span><br>
<span>In order to overcome the time costs of ICA I have been using EEGLab and a modified Batch plugin on the Shared Hierarchical Academic Research Computer Network (SHARCNet, <a href="http://www.sharcnet.ca/" target="_blank">www.sharcnet.ca</a>,
it is on my to-do-list to explore similar international HPC resources). While this does not necessarily speed up the ICA calculation it allows me to run up to 64 simultaneous Matlab workers (shared across users). I am also exploring Octave in this context
(no licensing limitations).</span><br>
<span></span><br>
<span>While presenting this strategy to the HPC community at a recent research day I was enthusiastically approached by someone who witnessed a GPU optimized ICA implemented in R. I have not had a chance to look into it further than finding this site<a href="http://brainarray.mbni.med.umich.edu/brainarray/rgpgpu/" target="_blank">http://brainarray.mbni.med.umich.edu/brainarray/rgpgpu/</a></span><br>
<span></span><br>
<span>See also<a href="http://sccn.ucsd.edu/wiki/GPU_and_EEGLAB" target="_blank">http://sccn.ucsd.edu/wiki/GPU_and_EEGLAB</a></span><br>
<br>
<div>___</div>
<div>Sent from an auto-correcting touch screen device.</div>
<div>___</div>
<div>James A. Desjardins, MA</div>
<div>Electrophysiology Technologist</div>
<div>Cognitive and Affective Neuroscience Lab, Psychology Department</div>
<div>Jack and Nora Centre for Lifespan Development Research</div><div class="im">
<div>Brock University</div>
<div>500 Glenridge Ave.</div>
</div><div>St. Catharine's, ON. Canada L2S 3A1</div>
<div><a href="tel:905-688-5550%20x4676" value="+19056885550" target="_blank">905-688-5550 x4676</a></div>
<div>___</div>
<div>"'Cause you never can tell What goes on down below!</div>
<div>"This pool might be bigger Than you or I know!"</div>
<div><br>
</div>
<div>McElligot's Pool</div>
<div>Dr. Seuss 1947</div>
</div><div><div class="h5">
<div><br>
On Jul 24, 2012, at 2:42 PM, "Baris Demiral" <<a href="mailto:demiral.007@googlemail.com" target="_blank">demiral.007@googlemail.com</a>> wrote:<br>
<br>
</div>
<div></div>
<blockquote type="cite">
<div><span>Hi James,</span><br>
<span></span><br>
<span>1- For frequency of interest of 200Hz, you can down-sample your data</span><br>
<span>down to 512Hz. But before that, low-pass filter your data with cut off</span><br>
<span>value of 250Hz or so. Follow Nyquist theorem.</span><br>
<span>2- You can run ICA on continuous data, but make sure you have marked</span><br>
<span>AND rejected the bad segments in the EEG data, since bad recording</span><br>
<span>WILL influence your ICA analysis A LOT. Pre-processing is still</span><br>
<span>important, even though ICA will eventually be used to reject artifacts</span><br>
<span>later. SO, observe your data well.</span><br>
<span>3- Xeon processors should have more than 2 cores I think. Run parallel</span><br>
<span>MATLABs on the same computer over the different cores for different</span><br>
<span>sets of subjects.</span><br>
<span></span><br>
<span>Arno, and other eeglab gurus, do you have any plans to</span><br>
<span>implement/combine ICA routines with parallel computing toolbox in</span><br>
<span>matlab? Is it possible to create, say, a PARICA? Is this</span><br>
<span>theoretically possible? For instance, ICA routine can divide the data</span><br>
<span>into 4 or so and then combine them over different cores/machines?</span><br>
<span></span><br>
<span>Cheers,</span><br>
<span>Baris</span><br>
<span></span><br>
<span>On Fri, Jul 13, 2012 at 1:07 PM, James Schaeffer <<a href="mailto:schaefj3@gmail.com" target="_blank">schaefj3@gmail.com</a>> wrote:</span><br>
<blockquote type="cite"><span>Hi All,</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>Thanks for your help. I have started using binica and it is going a bit</span><br>
</blockquote>
<blockquote type="cite"><span>faster. We have chosen to use a high sampling rate (2048 Hz) because we</span><br>
</blockquote>
<blockquote type="cite"><span>thought it might be needed for cross-frequency coupling analysis with high</span><br>
</blockquote>
<blockquote type="cite"><span>gamma up to 200 Hz. If I downsample, will I still be able to see these</span><br>
</blockquote>
<blockquote type="cite"><span>relationships?</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>Thanks again,</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>James</span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>On Thu, Jul 5, 2012 at 6:24 PM, James Schaeffer <<a href="mailto:schaefj3@gmail.com" target="_blank">schaefj3@gmail.com</a>> wrote:</span><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Dear eeglablist,</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>I am running ICAs on 10 minutes of Biosemi EEG data, collected from 128</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>channels, and sampled at 2048 Hz. However, the ICAs have been running for a</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>few days without much progress. Two computers have 8G RAM and an Intel(R)</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Xeon(TM) CPU 2.80GHz. One has been running an ICA for 6 days and is on step</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>33; the other, for 4 days, and is on step 28. Another computer has 12G RAM</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>and an Intel(R) Xeon(R) CPU 5110 @ 1.60GHz; it has been running for 3 days</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>and is on step 60. All are running openSUSE 12.1 (x86_64), with eeglab</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>version 10.2.2.4b. The 'free' command indicates that they are not using any</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>swap space. Should it be taking this long? Is it possible that we have</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>more than the one copy of the data in ram or that Matlab or Eeglab has</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>placed something else in ram, or is busy with other processes? Is there</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>anything I can do to speed up this process? Any help would be greatly</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>appreciated.</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span></span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>Thanks in advance,</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>James</span><br>
</blockquote>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span></span><br>
</blockquote>
<blockquote type="cite"><span>_______________________________________________</span><br>
</blockquote>
<blockquote type="cite"><span>Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">
http://sccn.ucsd.edu/eeglab/eeglabmail.html</a></span><br>
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<span></span><br>
<span></span><br>
<span></span><br>
<span>-- </span><br>
<span>Ş. Barış Demiral, PhD.</span><br>
<span>Department of Psychiatry</span><br>
<span>Washington University</span><br>
<span>School of Medicine</span><br>
<span>660 S. Euclid Avenue</span><br>
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<span>Phone: <a href="tel:%2B1%20%28314%29%20747%201603" value="+13147471603" target="_blank">+1 (314) 747 1603</a></span><br>
<span></span><br>
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