<div dir="ltr"><div class="gmail_quote"><div dir="ltr"><b id="m_-318448534952115577gmail-m_-2041195858289426243gmail-docs-internal-guid-fa7456b6-65b4-1326-227c-a867bb17b723" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><p dir="ltr" style="font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><br><span id="m_-318448534952115577gmail-m_-2041195858289426243gmail-docs-internal-guid-fa7456b6-65b4-1326-227c-a867bb17b723" style="text-align:start"></span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify;display:inline!important"><span style="font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">To achieve </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">high-resolution EEG source imaging</span><span style="font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> requires (a) </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">an accurate electrical head model</span><span style="font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">, and (b) </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">accurate co-registration of the scalp electrode positions to the head model</span><span style="font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">. 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></p></b><div><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify;display:inline!important"><span style="font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><br></span></p></b></div><div><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify;display:inline!important"><span style="font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><i>Without</i></span><span style="font-style:normal;font-weight:400;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> 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></p></b></div><div><div style="text-align:justify"><font face="Arial"><span style="font-size:12.6667px;white-space:pre-wrap"><br></span></font></div><b><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">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></p><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt;display:inline!important"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"></b></span></p><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><b style="font-size:small"></b></p><p></p><p></p></b><br><font face="arial, helvetica, 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="http://structure.io" 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).<br></font></div><div><br><p dir="ltr" style="font-weight:normal;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">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, </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><i>get_chanlocs</i></span><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">, is now available through the EEGLAB Extension Manager. A wiki page (</span><a href="http://sccn.ucsd.edu/wiki/get_chanlocs" style="font-style:normal;color:rgb(17,85,204);text-decoration:none" target="_blank"><span style="font-size:9.5pt;font-family:Arial;color:rgb(17,85,204);background-color:rgb(255,255,255);font-weight:400;font-style:italic;font-variant:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">sccn.ucsd.edu/wiki/get_chanlo<wbr>cs</span></a><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">) gives an overview, and a linked pdf user guide describes the process of using </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><i>get_chanlocs</i></span><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">. </span></p><br><p dir="ltr" style="text-align:start;text-indent:0px;text-decoration-style:initial;text-decoration-color:initial;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-variant-numeric:normal;font-variant-east-asian:normal;vertical-align:baseline">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<b><br><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;background-color:rgb(255,255,255);text-align:start;text-indent:0px"></b></b></span></p><p dir="ltr" style="font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><b><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;background-color:rgb(255,255,255);text-align:start;text-indent:0px"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial;font-size:12.8px;background-color:rgb(255,255,255)"></b></span></b></b></p><p></p><b><b style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;background-color:rgb(255,255,255);text-align:start;text-indent:0px"><b style="text-align:start"></b><p></p></b></b><p></p><b><p style="text-align:start;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Later, when the data are to be analyzed, the </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><i>get_chanlocs</i></span><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> 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 </span><span style="font-style:italic;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">EEG.chanlocs</span><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> structure. A montage template created for each montage used in a laboratory can be used by </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><i>get_chanlocs</i></span><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> as a reference during this process to speed and minimize human error during the electrode location measurement process.</span></p><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> </span></p><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Once the electrode positions have been stored in the dataset, further processes can use their positions for source localization and electric field plotting. </span></p><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"> </span></p><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">We thank Robert Oostenveld and the FieldTrip team for creating and sharing the basic functions used in </span><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"><i>get_chanlocs</i></span><span style="font-style:normal;font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">, 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></p><br><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Scott Makeig</span></p><span class="m_-318448534952115577gmail-HOEnZb" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal"><font color="#888888"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Clement Lee</span></p></font></span><br><p dir="ltr" style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:justify;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;font-style:normal;font-weight:normal;line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:9.5pt;font-family:Arial;color:rgb(34,34,34);background-color:rgb(255,255,255);font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">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></p></b><span class="HOEnZb"><font color="#888888"><br clear="all"><div><br></div>-- <br><div class="m_-318448534952115577gmail_signature" data-smartmail="gmail_signature">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="http://sccn.ucsd.edu/~scott" target="_blank">http://sccn.ucsd.edu/~scott</a></div>
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</div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">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="http://sccn.ucsd.edu/~scott" target="_blank">http://sccn.ucsd.edu/~scott</a></div>
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