[Eeglablist] [EXTERNAL] get_chanlocs - a new 3-D image-based electrode position digitizer app

Wed Nov 7 10:12:50 PST 2018

Thank you, I look forward to trying it out after I find the $ for the Structure Scanner and iPad.

To all: who in the community has been successful with this process?

-Jeff

From: Clement Lee <cll008 at eng.ucsd.edu>
Sent: Wednesday, November 07, 2018 9:51 AM
To: Eriksen, Jeff :LGS Neurodiagnostics <JEriksen at LHS.ORG>
Cc: eeglablist at sccn.ucsd.edu
Subject: Re: [Eeglablist] [EXTERNAL] get_chanlocs - a new 3-D image-based electrode position digitizer app

Thanks for your interest Jeff.

  1.  FT does not need to be separately installed. get_chanlocs includes necessary (slightly modified) files in a private folder.
  2.  There should not be any dependencies on other toolboxes. If some error occurs please let me know.

On Wed, Nov 7, 2018 at 8:56 AM Eriksen, Jeff :LGS Neurodiagnostics <JEriksen at lhs.org<mailto:JEriksen at lhs.org>> wrote:
This sound wonderful. Questions:

  1.  Is FieldTrip required to use get_chanlocs?
  2.  Are any Matlab toolboxes required to run get_chanlocs?

Trying to calculate total costs.

Thanks,
-Jeff

From: Eriksen, Jeffrey :LGS Neurodiagnostics
Sent: Tuesday, May 15, 2018 3:47 PM
To: K Jeff Eriksen <kjefferiksen at comcast.net<mailto:kjefferiksen at comcast.net>>
Subject: FW: [EXTERNAL][Eeglablist] get_chanlocs - a new 3-D image-based electrode position digitizer app

From: eeglablist [mailto:eeglablist-bounces at sccn.ucsd.edu] On Behalf Of Scott Makeig
Sent: Tuesday, May 15, 2018 3:41 PM
To: eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>
Subject: [EXTERNAL][Eeglablist] get_chanlocs - a new 3-D image-based electrode position digitizer app

This email originated from outside of Legacy Health. Please use CAUTION when clicking on links or opening documents.

To achieve high-resolution EEG source imaging requires (a) an accurate electrical head model, and (b) accurate co-registration of the scalp electrode positions to the head model. 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!).

Without 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.

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.

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 (structure.io<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>) 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).

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, get_chanlocs, is now available through the EEGLAB Extension Manager. A wiki page (sccn.ucsd.edu/wiki/get_chanlocs<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>) gives an overview, and a linked pdf user guide describes the process of using get_chanlocs.

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

Later, when the data are to be analyzed, the get_chanlocs 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 EEG.chanlocs structure. A montage template created for each montage used in a laboratory can be used by get_chanlocs as a reference during this process to speed and minimize human error during the electrode location measurement process.

Once the electrode positions have been stored in the dataset, further processes can use their positions for source localization and electric field plotting.

We thank Robert Oostenveld and the FieldTrip team for creating and sharing the basic functions used in get_chanlocs, 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.

Scott Makeig

Clement Lee

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.

--
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, http://sccn.ucsd.edu/~scott<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>

--
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, http://sccn.ucsd.edu/~scott<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>

--
Clement Lee
Applications Programmer
Swartz Center for Computational Neuroscience
Institute for Neural Computation, UC San Diego
858-822-7533
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