<p dir="ltr"><br>
Dear Stefania,<br>
you are correct. By interpolating channels we are decreasing the linear independency of the channels and this is where the rank-deficiency problem, discussed several times on the list, emerges. It is better to interpolate channels after ICA. Actually - EEGlab produces a warning when interpolation is performed on data without ICA weights.<br>
</p>
<p dir="ltr">@Valeri<br>
You are correct, but what Makoto was referring to is that any difference between two ICA decompositions on identical data - but one in continuous and other in epoched form - is not due to epoching (but the stochasticity of ICA).<br>
</p>
<div class="gmail_quote">11 wrz 2013 21:07, "<a href="mailto:sf.ang@libero.it">sf.ang@libero.it</a>" <<a href="mailto:sf.ang@libero.it">sf.ang@libero.it</a>> napisa³(a):<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p style="margin:0px;padding:0px">Hi all,</p><p style="margin:0px;padding:0px">I am wondering regarding the order of preprocessing.. is it really ok to interpolate bad channels before running ICA? Shouldn't we first run ICA only on the good channels and later interpolate bad ones which were excluded from the ICA?</p>
<p style="margin:0px;padding:0px">Thanks</p><p style="margin:0px;padding:0px">Stefania Ficarella</p><p style="margin:0px;padding:0px"><br></p><p style="margin:0px;padding:0px"><br></p><p style="margin:0px;padding:0px"><br>
</p>
<blockquote>
----Messaggio originale----<br>
Da: <a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a><br>
Data: 11/09/2013 3.06<br>
A: "Katherine Naish"<<a href="mailto:K.R.Naish@pgr.reading.ac.uk" target="_blank">K.R.Naish@pgr.reading.ac.uk</a>><br>
Cc: "<a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a>"<<a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a>><br>
Ogg: Re: [Eeglablist] Epoching eeg data<br>
<br>
<div dir="ltr">Dear Katherine,<div><br></div><div><span style="font-family:Tahoma;font-size:13.333333015441895px">> The previous messages largely answer my query, but I'd like just to make sure I understand correctly. The results of ICA decomposition should be similar whether the data is epoched or not- is that correct? </span></div>
<div><span style="font-family:Tahoma;font-size:13.333333015441895px"><br></span></div><div><span style="font-family:Tahoma;font-size:13.333333015441895px">Correct. If you have the same number of datapoint before and after epoching, ICA results should be as identical as the two results from running ICA twice on the same data.</span></div>
<div><br></div><div><span style="font-family:Tahoma;font-size:13.333333015441895px">> Obviously the results will be different if the data itself is different, but does ICA essentially treat epoched data as a continuous section?</span></div>
<div><font face="Tahoma"><br></font></div><div><div class="gmail_extra">ICA shuffles all datapoints as a preprocess; thus the concept of time disappears.</div><div class="gmail_extra"><br></div><div class="gmail_extra"><span style="font-family:Tahoma;font-size:13.333333015441895px">> My pre-processing order is the following: resample, filter, epoch, remove baseline, interpolate bad channels and remove bad epochs (based on visual inspection), re-reference to average, and (finally) run ICA to detect artefacts.</span></div>
<div class="gmail_extra"><span style="font-family:Tahoma;font-size:13.333333015441895px"><br></span></div><div class="gmail_extra"><span style="font-family:Tahoma">It looks ok.</span></div><div class="gmail_extra"><span style="font-family:Tahoma;font-size:13.333333015441895px"><br>
</span></div><div class="gmail_extra"><span style="font-family:Tahoma;font-size:13.333333015441895px">> One thing I wasn't sure about was re-referencing- am i doing that at the right point?</span><br></div><div class="gmail_extra">
<br></div><div class="gmail_extra">Yes.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Makoto</div><div class="gmail_extra"><br><div class="gmail_quote">2013/9/10 Katherine Naish <span dir="ltr"><<a href="mailto:K.R.Naish@pgr.reading.ac.uk" target="_blank">K.R.Naish@pgr.reading.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<p>Dear all,</p>
<p><br></p>
<p><br></p>
<p>The previous messages largely answer my query, but I'd like just to make sure I understand correctly. The results of ICA decomposition should be similar whether the data is epoched or not- is that correct? Obviously the results will be different if the data
itself is different, but does ICA essentially treat epoched data as a continuous section?</p>
<p><br></p>
<p>I would also really appreciate it if someone could approve, or otherwise, my pre-processing order. My pre-processing order is the following: resample, filter, epoch, remove baseline, interpolate bad channels and remove bad epochs (based on visual inspection),
re-reference to average, and (finally) run ICA to detect artefacts. One thing I wasn't sure about was re-referencing- am i doing that at the right point?</p>
<p><br></p>
<p>Many thanks in advance,</p>
<p>katherine</p>
<div>
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<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> <a href="mailto:eeglablist-bounces@sccn.ucsd.edu" target="_blank">eeglablist-bounces@sccn.ucsd.edu</a> [<a href="mailto:eeglablist-bounces@sccn.ucsd.edu" target="_blank">eeglablist-bounces@sccn.ucsd.edu</a>] on behalf of Miko³aj Magnuski [<a href="mailto:imponderabilion@gmail.com" target="_blank">imponderabilion@gmail.com</a>]<br>
<b>Sent:</b> 06 June 2013 19:13<br>
<b>Cc:</b> <a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a><br>
<b>Subject:</b> Re: [Eeglablist] Epoching eeg data<br>
</font><br>
</div><div><div>
<div></div>
<div>Dear Karlo,
<div><br>
</div>
<div>there is a case when dividing your whole 15 min. into smaller epochs (say 1 or 2 seconds long)</div>
<div>is quite convenient with respect to ICA:</div>
<div>--> cleaning data before ICA is easy if you just have to click bad epochs instead of marking</div>
<div>bad periods in continuous data - although this is just my personal feeling. </div>
<div>Nevertheless, you can also use automatic artifact rejection methods</div>
<div>available in EEGlab this way. These methods require epoched data. </div>
<div>(it is also easy to reconstruct your rejections later if you do them</div>
<div>on epochs - you can just <span>save the indices of windows that you removed [by </span></div>
<div>coping relevant field in EEG <span>structure after marking bad epochs</span><span>,</span></div>
<div><span>but before rejecting them]).</span></div>
<div><span>--> Then, after your first IC decomposition, if you are not satisfied with its results and observe that</span></div>
<div><span>some parts of your data may be responsible for poor results - you can remove</span></div>
<div><span>epochs containing these data easily and perform ICA again.</span></div>
<div><span><br>
</span></div>
<div><span>So, just as Makoto wrote, ICA does not care whether data are epoched<span></span> but you may -</span></div>
<div><span>because in some cases it is conven</span><span>ient in preprocessing or 'postprocessing' (correcting</span></div>
<div></div>
<div><span>ICA decomposition).</span></div>
<div><span>If you need any extra help with this - let me know (I have some scripts and functions to do this).</span></div>
<div><span><br>
</span></div>
<div><span>Mikolaj</span></div>
<div><span><br>
</span></div>
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<div><br>
W dniu ¶roda, 5 czerwca 2013 u¿ytkownik Makoto Miyakoshi napisa³:<br>
<blockquote style="border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid;margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">
<div dir="ltr">Dear Karlo,
<div><br>
</div>
<div>If you want to epoch your data into 3-min blocks, for example, put event markers every 3 minutes then epoch the data.</div>
<div><br>
</div>
<div>ICA does not care temporal continuity of the data since it shuffles them up differently for every iteration as a preprocess. That means, if the total number of datapoints are the same before and after the epoching, the ICA results should be the same.</div>
<div><br>
</div>
<div>Makoto</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/6/3 karlo gonzales <span dir="ltr"><<a href="https://dbxprd0111.outlook.com/owa/UrlBlockedError.aspx" target="_blank">thats_karlo@yahoo.com</a>></span><br>
<blockquote style="border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid;margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">
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<div><font face="arial, helvetica, sans-serif">Dear EEGlab experts,</font></div>
<div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><br>
</div>
<div style="background-color:transparent"><font face="arial, helvetica, sans-serif">I need you help regarding an</font><span style="background-color:transparent"><font face="arial, helvetica, sans-serif"> eeg data files which was recorded during eye closed
state (15 min long). Thus, there is no event to epoch the data. 1) How do you epoch such data</font></span><span style="background-color:transparent;font-style:normal;font-family:arial,helvetica,sans-serif;font-size:small">? 2) should we epoch data
before running ica (dose more epoch means better results?)</span></div>
<div style="background-color:transparent;font-style:normal;font-family:arial,helvetica,sans-serif;font-size:13px">
<font face="arial, helvetica, sans-serif">Thanks in advance</font></div>
</div>
</div>
<br>
_______________________________________________<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Makoto Miyakoshi<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, University of California San Diego<br>
</div>
</div>
</blockquote>
</div>
<br>
<br>
-- <br>
Pozdrawiam,<br>
Miko³aj Magnuski<br>
</div>
</div></div></div>
</div>
</div>
<br>_______________________________________________<br>
Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
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<div><br></div>
-- <br><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div>
</div></div></div>
<br>
</blockquote><p><br></p><br>_______________________________________________<br>
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