<div dir="ltr">Dear Jumana,<div><br></div><div>AMICA does not do any drastic improvement compared with infomax. So if you saw bad results in infomax (runica), AMICA would return the bad results as well.</div><div><br></div><div>> Is it nexeeeary for me to change to amica?</div><div><br></div><div>If you say you have time and effort resource to do it, yes it is worth. But again, you should not expect any drastic changes in results. Remember GIGO: garbage in, garbage out.</div><div><br></div><div>> Also, if you do interpolate ICA then how many channels do you remove to prevent rank deficiency and how does this depend on the number of channels interpolated?<br></div><div><br></div><div>First of all, you never interpolate ICA activations. You can interpolate channels because it is less important information than IC sources, and the purpose of channel interpolation is ONLY FOR spatially-unbiased average referencing.</div><div><br></div><div>From UA49 to Newark,</div><div><br></div><div>Makoto</div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 13, 2017 at 1:28 AM, Ahmad, Jumana <span dir="ltr"><<a href="mailto:jumana.ahmad@kcl.ac.uk" target="_blank">jumana.ahmad@kcl.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Dear Makoto,<br>
I also noticed EEG lab have changed to AMICA but I've already run ICA on 100 participants using the previously recommended runica. I was never rank deficient (i average ref after ICA).
<br>
I do it have component corruption. Is it nexeeeary for me to change to amica? It would mean redoing work.<br>
Also, if you do interpolate ICA then how many channels do you remove to prevent rank deficiency and how does this depend on the number of channels interpolated?<span class="gmail-"><br>
Best wishes,<br>
Jumana <br>
------------------------------<wbr>------------<br>
Jumana Ahmad<br>
Post-Doctoral Research Worker in Cognitive Neuroscience<br>
EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study<br>
Room M1.26.Department of Forensic and Neurodevelopmental Sciences (PO 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College London | 16 De Crespigny Park | London SE5 8AF<br>
<br>
Phone: 0207 848 5359| Email: <a href="mailto:jumana.ahmad@kcl.ac.uk" target="_blank">jumana.ahmad@kcl.ac.uk</a> | Website: <a href="http://www.eu-aims.eu" target="_blank">www.eu-aims.eu</a> | Facebook: <a href="http://www.facebook.com/euaims" target="_blank">www.facebook.com/euaims</a><br>
<br>
<hr style="display:inline-block;width:98%">
</span><div id="gmail-m_8272730243121776340divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Ahmad, Jumana<br>
<b>Sent:</b> 13 January 2017 11:22:18<br>
<b>To:</b> <a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a><div><div class="gmail-h5"><br>
<b>Cc:</b> <a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a><br>
<b>Subject:</b> Re: [Eeglablist] ICA, re-referencing, interpolation</div></div></font>
<div> </div>
</div><div><div class="gmail-h5">
<div><br>
Hi Makoto,<br>
I think your code does, but I am following a mix of your pipeline when appropriate but also reordering this it to keep in line with what my colleagues in the same project are doing, and they interpolate after. So I am trying to follow those steps. I am hoping
that if I delete the ICA information and then interpolate and rereference the raw data,that this should be fine? I will check carefully but when I view the raw data after rereferencing, the blinks are still removed.
<br>
Best wishes,<br>
Jumana<br>
------------------------------<wbr>------------<br>
Jumana Ahmad<br>
Post-Doctoral Research Worker in Cognitive Neuroscience<br>
EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study<br>
Room M1.26.Department of Forensic and Neurodevelopmental Sciences (PO 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College London | 16 De Crespigny Park | London SE5 8AF<br>
<br>
Phone: 0207 848 5359| Email: <a href="mailto:jumana.ahmad@kcl.ac.uk" target="_blank">jumana.ahmad@kcl.ac.uk</a> | Website: <a href="http://www.eu-aims.eu" target="_blank">www.eu-aims.eu</a> | Facebook: <a href="http://www.facebook.com/euaims" target="_blank">www.facebook.com/euaims</a><br>
<br>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_8272730243121776340divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br>
<b>Sent:</b> 13 January 2017 10:02:59<br>
<b>To:</b> Ahmad, Jumana<br>
<b>Cc:</b> <a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a><br>
<b>Subject:</b> Re: [Eeglablist] ICA, re-referencing, interpolation</font>
<div> </div>
</div>
<div>
<div dir="ltr">Dear Jumana,
<div><br>
</div>
<div>> I am trying to replicate a pipeline very precisely and this pipeline interpolates after ICA.<br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Oops, is that true? But when I checked the latest description now, I found that they do NOT change channels after AMICA. Press 'refresh' button to update the page if you haven't done so.</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">> If possible I would like to interpolate after, as I only need to work with the channel data after the ICA. <br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">If that's the goal, then I think it's fine. But test it carefully before you press the final button! If you are not confident, I recommend you use dead copy of my code and use the channel information in the end (assuming that my latest
code does NOT interpolate channels after ICA).</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Makoto</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jan 12, 2017 at 11:31 PM, Ahmad, Jumana <span dir="ltr">
<<a href="mailto:jumana.ahmad@kcl.ac.uk" target="_blank">jumana.ahmad@kcl.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><br>
Hi Makoto,<br>
I am trying to replicate a pipeline very precisely and this pipeline interpolates after ICA. I only wanted to remove the artefacts from the data and then convert back to channel data. If I delete the eye blink components and then convert back to raw data, -and
then delete all ICA info, such as the weights and activations etc, is it then safe for me to interpolate using the channel data (which now has blinks removed)?<br>
<br>
If I really have to avoid the situation, then how do you get around rank issues of interpolating before? I know you delete channels but how do you know how many to delete in relation to the number of channels interpolated. If possible I would like to interpolate
after, as I only need to work with the channel data after the ICA. <br>
<br>
Thank you again for your advice! Very much appreciated. <br>
<span class="gmail-m_8272730243121776340gmail-">Jumana <br>
------------------------------<wbr>------------<br>
Jumana Ahmad<br>
Post-Doctoral Research Worker in Cognitive Neuroscience<br>
EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study<br>
</span>Room M1.26.Department of Forensic and Neurodevelopmental Sciences (PO 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College London | 16 De Crespigny Park | London SE5 8AF<br>
<br>
Phone: 0207 848 5359| Email: <a href="mailto:jumana.ahmad@kcl.ac.uk" target="_blank">
jumana.ahmad@kcl.ac.uk</a> | Website: <a href="https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eu-aims.eu&data=01%7C01%7Cjumana.ahmad%40kcl.ac.uk%7C89d274d92ca94825ded208d43b8ab8d2%7C8370cf1416f34c16b83c724071654356%7C0&sdata=b2bm%2BLN%2BqlU%2Ff%2BfqHuP1cDUBtGGS8VSHrYwdKzl5d8A%3D&reserved=0" target="_blank">
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<hr style="display:inline-block;width:98%">
<div id="gmail-m_8272730243121776340gmail-m_-7367123479538496963divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br>
<b>Sent:</b> 13 January 2017 08:05:04<br>
<b>To:</b> Ahmad, Jumana<br>
<b>Cc:</b> <a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a><br>
<b>Subject:</b> Re: [Eeglablist] ICA, re-referencing, interpolation</font>
<div> </div>
</div>
<div>
<div class="gmail-m_8272730243121776340gmail-h5">
<div>
<div dir="ltr">Dear Jumana,
<div><br>
</div>
<div>I encountered that kind of situation many times, which is why I thought it would be a nice idea to show the exact steps in the wiki page. Now you see my point!</div>
<div><br>
</div>
<div>Editing channels after ICA is DANGEROUS. There are even some phenomena that confused me to death which I still don't understand (and do not remember well any more). Some of EEGLAB's check function can detect the change of channel number difference and
inconsistency with EEG.ica-items, but not all the operations are not supported, particualy any behavior outside GUI (but the worst mysterious case I experienced was replicated even using GUI, so I guess it was like I was performing bug finding in EEGLAB, as
if several test players plays an alpha version of a computer game trying to do the weirdest things to find bugs.)</div>
<div><br>
</div>
<div>So, my advice is that DO NOT EDIT CHANNELS AFTER ICA. Once the mixing matrix is confused and how it happened, you are done. Just stay away from that situation.</div>
<div><br>
</div>
<div>I appreciate though you have been doing exploration! I'm glad to see that at least other guys than I experience the same issues. </div>
<div><br>
</div>
<div>From Lufthansa455 to Frankfurt,</div>
<div><br>
</div>
<div>Makoto</div>
<div><br>
</div>
<div><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 4, 2017 at 9:06 AM, Ahmad, Jumana <span dir="ltr">
<<a href="mailto:jumana.ahmad@kcl.ac.uk" target="_blank">jumana.ahmad@kcl.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-GB">
<div class="gmail-m_8272730243121776340gmail-m_-7367123479538496963m_-3838460540513318786WordSection1">
<p class="MsoNormal">Dear EEGLab,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I do not include noisy channels in ICA which I only do to remove eye related components, and specifically want to interpolate then after ICA for rank reasons. I have now done this to over 100 datasets.
<u></u><u></u></p>
<p class="MsoNormal">However, once I interpolate and then re-reference my data to the average, I get the error: Error: some channels not used for ICA decomposition are used for rereferencing<u></u><u></u></p>
<p class="MsoNormal"> the ICA decomposition has been removed<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">However, I purposefully wanted to interpolate these after ICA, and then use them for the average.<u></u><u></u></p>
<p class="MsoNormal">Is my eye-blink removal via ICA now affected and undone? <u>
</u><u></u></p>
<p class="MsoNormal">I would appreciate any advice.<u></u><u></u></p>
<p class="MsoNormal">Best wishes,<u></u><u></u></p>
<p class="MsoNormal">Jumana <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<span style="font-size:10pt;color:rgb(31,73,125)">Post-Doctoral Research Worker in Cognitive Neuroscience </span><span style="font-family:helvetica,sans-serif;color:black"><u></u><u></u></span></p>
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<i><span style="font-size:10pt;color:rgb(31,73,125)">EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study</span></i><span style="font-family:helvetica,sans-serif;color:black"><u></u><u></u></span></p>
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<span style="font-size:10pt;color:rgb(31,73,125)">Room M1.09. Department of Forensic and Neurodevelopmental Sciences (PO 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College London | 16 De Crespigny Park | London SE5 8AF</span><span style="font-family:helvetica,sans-serif;color:black"><u></u><u></u></span></p>
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</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail-m_8272730243121776340gmail-m_-7367123479538496963gmail_signature">
<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>
</div>
</div>
</div>
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</blockquote>
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<br>
<br clear="all">
<div><br>
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-- <br>
<div class="gmail-m_8272730243121776340gmail_signature">
<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>
</div>
</div>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><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>