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<p class="MsoNormal">Thank you, I look forward to trying it out after I find the $ for the Structure Scanner and iPad.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">To all: who in the community has been successful with this process?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-Jeff<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b>From:</b> Clement Lee <cll008@eng.ucsd.edu> <br>
<b>Sent:</b> Wednesday, November 07, 2018 9:51 AM<br>
<b>To:</b> Eriksen, Jeff :LGS Neurodiagnostics <JEriksen@LHS.ORG><br>
<b>Cc:</b> eeglablist@sccn.ucsd.edu<br>
<b>Subject:</b> Re: [Eeglablist] [EXTERNAL] get_chanlocs - a new 3-D image-based electrode position digitizer app<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Thanks for your interest Jeff. <o:p></o:p></span></p>
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<span style="font-family:"Times New Roman",serif">FT does not need to be separately installed. get_chanlocs includes necessary (slightly modified) files in a private folder.</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1">
<span style="font-family:"Times New Roman",serif">There should not be any dependencies on other toolboxes. If some error occurs please let me know.</span><o:p></o:p></li></ol>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, Nov 7, 2018 at 8:56 AM Eriksen, Jeff :LGS Neurodiagnostics <<a href="mailto:JEriksen@lhs.org">JEriksen@lhs.org</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This sound wonderful. Questions:<o:p></o:p></p>
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Is FieldTrip required to use get_chanlocs?<o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo2">
Are any Matlab toolboxes required to run get_chanlocs?<o:p></o:p></li></ol>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Trying to calculate total costs.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">-Jeff<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>From:</b> Eriksen, Jeffrey :LGS Neurodiagnostics
<br>
<b>Sent:</b> Tuesday, May 15, 2018 3:47 PM<br>
<b>To:</b> K Jeff Eriksen <<a href="mailto:kjefferiksen@comcast.net" target="_blank">kjefferiksen@comcast.net</a>><br>
<b>Subject:</b> FW: [EXTERNAL][Eeglablist] get_chanlocs - a new 3-D image-based electrode position digitizer app<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>From:</b> eeglablist [<a href="mailto:eeglablist-bounces@sccn.ucsd.edu" target="_blank">mailto:eeglablist-bounces@sccn.ucsd.edu</a>]
<b>On Behalf Of </b>Scott Makeig<br>
<b>Sent:</b> Tuesday, May 15, 2018 3:41 PM<br>
<b>To:</b> <a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a><br>
<b>Subject:</b> [EXTERNAL][Eeglablist] get_chanlocs - a new 3-D image-based electrode position digitizer app<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:red">This email originated from outside of Legacy Health. Please use CAUTION when clicking on links or opening documents.</span>
<o:p></o:p></p>
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<p style="margin-bottom:12.0pt;text-align:justify"><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt;text-align:justify;display:inline!important">
<span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">To achieve
<b>high-resolution EEG source imaging</b> requires (a) <b>an accurate electrical head model</b>, and (b)
<b>accurate co-registration of the scalp electrode positions to the head model</b>. Several packages are available for fashioning a geometrically accurate head model from an anatomic MR head image. We use Zeynep Akalin Acar's Neuromagnetic Forward problem Toolbox
(NFT), which she is now coupling to the first non-invasive, universally applicable method (SCALE) for estimating individual skull conductivity from EEG data (Akalin Acar et al., 2016; more news of this soon!).
</span><o:p></o:p></p>
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<p style="margin-bottom:12.0pt;text-align:justify;display:inline!important"><b><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white"> </span></b><o:p></o:p></p>
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<i><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">Without</span></i><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white"> a subject MR head image, equivalent dipole models for
independent component brain sources need to use a (good) template head model. Zeynep has shown that the dipole localization process is more accurate when the template head is warped to fit the recorded 3-D positions of the electrodes -- IF these are recorded
accurately. </span><o:p></o:p></p>
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<span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">For too long, it has been both expensive and time consuming (for both experimenter and subject) to record the 3-D positions of the scalp electrodes for each subject.
Magnetic and ultrasound wand systems to do this require the subject to sit patiently while the experimenter clicks on the 3-D position of each electrode. In recent years, however, cameras capable of recording images in 3-D have appeared and are now becoming
cheaper and more prevalent. </span><o:p></o:p></p>
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<span style="font-family:"Arial",sans-serif">Robert Oostenveld, originator of the FieldTrip toolbox, alerted us that he and his students in Nijmegen had added functions to FieldTrip to compute the 3-D positions of scalp electrodes from scanned 3-D images acquired
by one such (suitable and quite easy to use) camera, the Structure scanner (<a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fstructure.io&data=02%7C01%7CJEriksen%40lhs.org%7Cd03001e31d644b2e426308d644d9a227%7C3683988d7d404338bf200b5dd13f4301%7C0%7C0%7C636772098853368468&sdata=LLzeJh%2FqaHT4lnU3U6HD75NfI1mlqnu6g%2BVzdZ6QdlE%3D&reserved=0" target="_blank">structure.io</a>)
mounted to an Apple iPad. The 3-D head scanning process greatly minimizes (to seconds) the time spent by the subject snd experimenter on electrode position recording, while also minimizing the position-measuring system cost (currently to near $1000).</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"> <o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt;text-align:justify;background:white"><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">Because of the importance of widespread adoption of electrode position recording to advancing
EEG source imaging, I asked Clement Lee at SCCN to build and test a gui-based EEGLAB plug-in incorporating this new approach. The new plug-in,
<i>get_chanlocs</i>, is now available through the EEGLAB Extension Manager. A wiki page (</span><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222"><a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsccn.ucsd.edu%2Fwiki%2Fget_chanlocs&data=02%7C01%7CJEriksen%40lhs.org%7Cd03001e31d644b2e426308d644d9a227%7C3683988d7d404338bf200b5dd13f4301%7C0%7C0%7C636772098853378476&sdata=gph9JukZTQEpKuv9ziIBy4fqinOjftontP8h4iec6xI%3D&reserved=0" target="_blank"><i><span style="color:#1155CC;background:white">sccn.ucsd.edu/wiki/get_chanlocs</span></i></a><span style="background:white">)
gives an overview, and a linked pdf user guide describes the process of using <i>
get_chanlocs</i>. </span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"> <o:p></o:p></p>
<p style="margin-bottom:12.0pt">In brief, the process is as follows: a 3-D head image (3-D head ‘scan’) of the subject wearing the electrode cap is acquired using the Structure scanner; this image acquisition typically requires less than a minute to perform.
The resulting 3-D .obj image file is then stored with the data<o:p></o:p></p>
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<span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">Later, when the data are to be analyzed, the
<i>get_chanlocs</i> plug-in, called from the Matlab command line or EEGLAB menu, guides the data analyst through the process of loading the 3-D image and then clicking on each of the electrodes in the image (in the suggested order) to compute and store their
relative 3-D positions. (Note: in future this step will likely be automated using machine vision methods). The electrode labels and their 3-D positions relative to three skull landmarks (‘fiducial points’) are then written directly into the dataset
<i>EEG.chanlocs</i> structure. A montage template created for each montage used in a laboratory can be used by
<i>get_chanlocs</i> as a reference during this process to speed and minimize human error during the electrode location measurement process.</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt;text-align:justify;background:white;font-variant-ligatures:normal;font-variant-caps:normal;text-decoration-style:initial;text-decoration-color:initial;word-spacing:0px">
<span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">Once the electrode positions have been stored in the dataset, further processes can use their positions for source localization and electric field plotting.
</span><o:p></o:p></p>
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<span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">We thank Robert Oostenveld and the FieldTrip team for creating and sharing the basic functions used in
<i>get_chanlocs</i>, and urge that forward-looking EEG laboratories strongly consider adopting 3-D electrode montage image scanning when acquiring their data so as to enable high-resolution source imaging of the data -- in the near term and/or in future.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"><b> </b><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt;text-align:justify;background:white"><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">Scott Makeig</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt;text-align:justify"><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">Clement Lee</span><o:p></o:p></p>
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<p style="margin:0in;margin-bottom:.0001pt;text-align:justify;background:white"><span style="font-size:9.5pt;font-family:"Arial",sans-serif;color:#222222;background:white">p.s. As always, we are interested in feedback concerning any bugs or feature suggestions.
It is best to use the EEGLAB Bugzilla facility for this.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888">Scott Makeig, Research Scientist and Director, Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California
San Diego, La Jolla CA 92093-0961, <a href="https://na01.safelinks.protection.outlook.com/?url=http:%2F%2Fsccn.ucsd.edu%2F~scott&data=02%7C01%7CJEriksen%40lhs.org%7Cd03001e31d644b2e426308d644d9a227%7C3683988d7d404338bf200b5dd13f4301%7C0%7C0%7C636772098853378476&sdata=9BjveVVncQL%2F08QrQftlVxAFtOssgH7X%2BY93Zu3L06c%3D&reserved=0" target="_blank">
http://sccn.ucsd.edu/~scott</a></span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Scott Makeig, Research Scientist and Director, Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla CA 92093-0961,
<a href="https://na01.safelinks.protection.outlook.com/?url=http:%2F%2Fsccn.ucsd.edu%2F~scott&data=02%7C01%7CJEriksen%40lhs.org%7Cd03001e31d644b2e426308d644d9a227%7C3683988d7d404338bf200b5dd13f4301%7C0%7C0%7C636772098853388485&sdata=t54O5KyMcbEFi8l%2BiTNba9NDfGxDASRH%2FtdRk6FVBqI%3D&reserved=0" target="_blank">
http://sccn.ucsd.edu/~scott</a><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Garamond",serif;color:black">Clement Lee</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Garamond",serif;color:black">Applications Programmer<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, UC San Diego<br>
858-822-7533</span><o:p></o:p></p>
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