<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I've not totally figured this out either - when running ICA against a Study, i don't seem to be able to save the ICA weights. If I edit the Study and check resave datasets.. the message says they haven't changed, don't need to be resaved.. and saving the Study itself explicitly doesn't seem to save ICA weights either... <div><br></div><div>What am I doing wrong? :)</div><div><br></div><div>thanks,</div><div>andrew</div><div><br><div><div>On Aug 19, 2009, at 9:22 AM, Keith Yoder wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Since two of us have encountered this issue before, it's probably worth posting this to list. <br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Keith Yoder</b> <span dir="ltr"><<a href="mailto:kjyoder@gmail.com">kjyoder@gmail.com</a>></span><br> Date: Thu, Aug 13, 2009 at 5:21 PM<br>Subject: Re: [Eeglablist] ICA weights not "saved"?<br>To: Andrew Hill <<a href="mailto:andrewhill@ucla.edu">andrewhill@ucla.edu</a>><br><br><br><div>In our case, we have to restrict the amount of data that ICA is working with to produce sensible components, but this is certainly driven in large-part by our paradigm. We are having subjects play a video game that consists of four distinct minigames, each of which has one or more cognitive tasks built into it (for more information see <a href="http://autismcollaborative.org" target="_blank">http://autismcollaborative.org</a>). </div> <div>This has given us very large datasets (128 channels recording for an hour). I thought this would be great - ICA would have a *lot* of data to work with. However, this means that the specfic events we are interested in comprise a very small proportion of the EEG data individually. For instance, a go-no-go task in one of the minigames occurs less than 60 times per game. If I'm assuming that the salient effects in the EEG occur within a three second window at each event, then I'm expecting ICA to pick out components that may only be active for for a total of 3 minutes out of the hour.<br> </div><div></div> <div>-Keith</div><div><div class="h5"><br><div class="gmail_quote">On Thu, Aug 13, 2009 at 4:40 PM, Andrew Hill <span dir="ltr"><<a href="mailto:andrewhill@ucla.edu" target="_blank">andrewhill@ucla.edu</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div style="word-wrap:break-word">hi Keith,<div><br></div><div>thanks for the reply - explicitly saving after ICA weights are calculated is what i was missing.</div><div><br></div><div>on running the ICA on epochs versus continuous recordings.. I was under the impression that Arno and Scott encouraged running ICA on the "longest" data chunks possible, and that running them on epochs would actually produce artifacts at the edges of the epoch.. are you not finding this?</div> <div><br></div><div>best,</div><div>andrew</div><div><div><div><br><div><div>On Aug 11, 2009, at 5:41 AM, Keith Yoder wrote:</div><br><blockquote type="cite"><div>I had a similar experience at first. Here's my resolution:<br> </div><div>Once Run ICA is finished, manually save the component-weighted datset. This can be done by either 'File -> save current dataset(s) as' or, if you are using a script, the pop_saveset(EEG) command.</div> <div>A rough outline of our process:</div><div>Import the dataset</div><div>Highpass filter the dataset</div><div>Save that filtered dataset</div><div>Extract epochs</div><div>Save the epoched datasets</div> <div>Run ICA</div> <div>Save the component-weighted epoched datasets</div><div>We've found that running ICA before epoching the datasets yields nonsensical results. Additionally, if you epoch the data first, then the ICA algorithm will only have to work on the data surrounding your event of interest. This will can greatly reduce the amount of time required for the algorithm to identify components. If your events are widely spaced throughout the dataset, you may even be able to include all of your channels at once.</div> <div>Hope this helps! If you have any questions, feel free to let me know.</div><div>-Keith</div><div>Research Aide</div><div>Belmonte Autism Lab</div><div>Cornell University</div><br><div class="gmail_quote"> On Mon, Aug 10, 2009 at 3:49 PM, Andrew Hill <span dir="ltr"><<a href="mailto:andrewhill@ucla.edu" target="_blank">andrewhill@ucla.edu</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> hi folks,<br> <br> i might be misunderstanding something about how the "Run ICA" works.<br> i've been running ICA against .set files, half of the channels at a<br> time to avoid out of memory errors... i got through all my .sets, and<br> then extracted epochs from all the .set files, assuming the ICA<br> weights would be inherited by the epochs.<br> <br> the problem is, when i open one of these .set files, it appears that<br> the data file doesn't actually have ICA weights saved into it. am i<br> doing something wrong?? is there some step to explicitly save the<br> weights with the .set file that i need to do?<br> <br> these weights don't appear to be saved even with the "write ICA<br> activations to disk" option checked...<br> <br> i cannot load more than one .set into memory at a time... and i cannot<br> process more than half the channels in one Run ICA go.. so what am i<br> missing? why are these not saved to the .set?<br> <br> thanks,<br> andrew<br> <br> _______________________________________________<br> Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br> To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br> For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a><br> </blockquote></div><br></blockquote></div><br></div></div></div></div></blockquote></div><br> </div></div></div><br> _______________________________________________<br>Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a></blockquote></div><br></div></body></html>