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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Many thanks to you both! It seems possible that in my first attempt there was some issue with 3d to 2d conversion - the back row of electrodes seemed folded 'under' and ended up
towards the center of the projection?
<div><br>
</div>
<div>Anyway, I'm moving forward with the current layout - thank you again!</div>
<div><br>
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<div id="divRpF239844" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> mne_analysis-bounces@nmr.mgh.harvard.edu [mne_analysis-bounces@nmr.mgh.harvard.edu] on behalf of Jaakko Leppakangas [jaeilepp@gmail.com]<br>
<b>Sent:</b> Wednesday, February 15, 2017 8:32 AM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] EGI sensor layout<br>
</font><br>
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<div>I believe that the problem here was actually the montage reader. The channel names were read incorrectly in mne versions 0.12 and older, causing duplicate channel names. So updating mne to the latest version should fix the problem. The workflow looks correct.<br>
<br>
</div>
HTH<br>
</div>
-Jaakko<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Feb 14, 2017 at 10:01 PM, Aaron Newman <span dir="ltr">
<<a href="mailto:Aaron.Newman@dal.ca" target="_blank">Aaron.Newman@dal.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">Hi Emily
<div><br>
</div>
<div>The plot you showed from MNE in your original post is the layout map for the much-older GSN 200 2.1 nets. For the past many years (decade?) EGI has sold the HCGSN nets, which have a slightly different layout (as shown in the "official" EGI layout you attached).
As you noticed, a telltale sign is whether the bottom-most centre electrode in the layout map is 81 (new) or 82 (old). </div>
<div><br>
</div>
<div>I haven't tried importing EGI data into MNE yet, so I can't speak directly to your issue. However I do know that EEGLAB for years (and possibly still) by default uses the old layout when using their EGI importer. The EEGLAB folks did, however, post a layout
map file for the new HCGSN configuration, which you can find at <a href="https://sccn.ucsd.edu/bugzilla/show_bug.cgi?id=1643" target="_blank">https://sccn.ucsd.edu/<wbr>bugzilla/show_bug.cgi?id=1643</a> It should be in a standard format that hopefully MNE
recognizes, or could be adapted pretty easily. Getting EGI data into MNE has been on my to-do list but I haven't tried it yet!</div>
<div><br>
Best,</div>
<div>Aaron</div>
</div>
<div>
<div class="h5"><br>
<div class="gmail_quote">
<div dir="ltr">On Tue, 14 Feb 2017 at 12:55 Emily Ruzich <<a href="mailto:Emily.Ruzich@neuro.gu.se" target="_blank">Emily.Ruzich@neuro.gu.se</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg" style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">
Hi Jaakko,
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg">I think we may have resolved this? The updated code is </div>
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">file
= '/Users/delfin/Documents/<wbr>RPKPILOT/RAW/PILOT002_GONOGO.<wbr>set'</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">###
read channel names and get raw data</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">mon
= mne.channels.read_montage('<wbr>GSN-HydroCel-128')</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">raw
= mne.io.read_raw_eeglab(file, preload=True)</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">raw.set_montage(mon)
## !!</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">###
look at channels</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">mne.viz.plot_sensors(<a href="http://raw.info" class="m_6877872554708086227gmail_msg" target="_blank">raw.info</a>,
show_names=True)</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">raw.plot_sensors(show_names=<wbr>True)</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt">raw.plot_sensors('3d')</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<font class="m_6877872554708086227gmail_msg" face="Calibri" size="3"><span class="m_6877872554708086227gmail_msg" style="font-size:12pt"><font class="m_6877872554708086227gmail_msg" size="2"><span class="m_6877872554708086227gmail_msg" style="font-size:11pt"><br class="m_6877872554708086227gmail_msg">
</span></font></span></font></div>
<div class="m_6877872554708086227gmail_msg" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif; font-size:medium; background-color:rgb(255,255,255); margin:0px">
<div class="m_6877872554708086227gmail_msg" style="font-family:Tahoma; font-size:13.3333px">
Sorry for any confusion! Hopefully we are correct and this is the right layout!</div>
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
</div>
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<hr class="m_6877872554708086227gmail_msg">
<div id="m_6877872554708086227m_8153990789109468078divRpF433620" class="m_6877872554708086227gmail_msg" style="direction:ltr">
<font class="m_6877872554708086227gmail_msg" face="Tahoma" color="#000000" size="2"><b class="m_6877872554708086227gmail_msg">From:</b>
<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="m_6877872554708086227gmail_msg" target="_blank">
mne_analysis-bounces@nmr.mgh.<wbr>harvard.edu</a> [<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="m_6877872554708086227gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.<wbr>harvard.edu</a>] on behalf of Jaakko Leppakangas [<a href="mailto:jaeilepp@gmail.com" class="m_6877872554708086227gmail_msg" target="_blank">jaeilepp@gmail.com</a>]<br class="m_6877872554708086227gmail_msg">
<b class="m_6877872554708086227gmail_msg">Sent:</b> Tuesday, February 14, 2017 3:14 PM<br class="m_6877872554708086227gmail_msg">
<b class="m_6877872554708086227gmail_msg">To:</b> Discussion and support forum for the users of MNE Software<br class="m_6877872554708086227gmail_msg">
<b class="m_6877872554708086227gmail_msg">Subject:</b> Re: [Mne_analysis] EGI sensor layout<br class="m_6877872554708086227gmail_msg">
</font><br class="m_6877872554708086227gmail_msg">
</div>
</div>
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<div class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg" style="font-family:Times New Roman; color:#000000; font-size:16px">
<div class="m_6877872554708086227gmail_msg"></div>
<div class="m_6877872554708086227gmail_msg">
<div dir="ltr" class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg">Hi Emily, <br class="m_6877872554708086227gmail_msg">
</div>
<br class="m_6877872554708086227gmail_msg">
</div>
I'm unable to replicate this. Looks like some channels are missing from your plot. Can you copy-paste the commands you run to plot this figure?<br class="m_6877872554708086227gmail_msg">
<br class="m_6877872554708086227gmail_msg">
</div>
-Jaakko<br class="m_6877872554708086227gmail_msg">
</div>
<div class="gmail_extra m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
<div class="gmail_quote m_6877872554708086227gmail_msg">On Tue, Feb 14, 2017 at 2:28 PM, Emily Ruzich
<span dir="ltr" class="m_6877872554708086227gmail_msg"><<a href="mailto:Emily.Ruzich@neuro.gu.se" class="m_6877872554708086227gmail_msg" target="_blank">Emily.Ruzich@neuro.gu.se</a>></span> wrote:<br class="m_6877872554708086227gmail_msg">
<blockquote class="gmail_quote m_6877872554708086227gmail_msg" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div class="m_6877872554708086227gmail_msg">
<div class="m_6877872554708086227gmail_msg" style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">
Hello all,
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg">I have a question about the sensor layout map for EGI hydrocel sensor nets.</div>
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg">I have been studying the two figures attached - one is the 128 channel map provided by EGI, the other is the sensor positions determined by using the commands mne.channels.read_montage('<wbr>GSN-HydroCel-128') and
mne.viz.plot_sensors.</div>
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg">While there are similarities, some definite differences exist - notably, 81 has shifted from the occipital midline to close to the vertex. Has this been addressed before? And if so, what is the advice you recommend?</div>
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg">Many thanks!</div>
<span class="m_6877872554708086227m_8153990789109468078HOEnZb m_6877872554708086227gmail_msg"><font class="m_6877872554708086227gmail_msg" color="#888888">
<div class="m_6877872554708086227gmail_msg">Emily</div>
<div class="m_6877872554708086227gmail_msg"><br class="m_6877872554708086227gmail_msg">
</div>
<div class="m_6877872554708086227gmail_msg"><span class="m_6877872554708086227gmail_msg" style="font-size:10pt"><br class="m_6877872554708086227gmail_msg">
</span></div>
</font></span></div>
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<br>
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<p dir="ltr" style="line-height:1.2; margin-top:0pt; margin-bottom:0pt"><span style="font-size:12px; font-family:arial; color:rgb(241,194,50); font-weight:700; vertical-align:baseline; white-space:pre-wrap; background-color:transparent">DALHOUSIE UNIVERSITY</span></p>
<p dir="ltr" style="line-height:1.2; margin-top:0pt; margin-bottom:0pt"><a href="http://ncil.science/" style="text-decoration:none" target="_blank"><span style="font-size:12px; font-family:arial; color:rgb(102,102,102); text-decoration:underline; vertical-align:baseline; white-space:pre-wrap; background-color:transparent">NCIL.science</span></a></p>
<a href="http://www.dal.ca/RADIANT" style="text-decoration:none" target="_blank"><span style="font-size:12px; font-family:arial; color:rgb(102,102,102); text-decoration:underline; vertical-align:baseline; white-space:pre-wrap; background-color:transparent">dal.ca/RADIANT</span></a></span><br>
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