[Eeglablist] Registering EGI 128 Channel GSN Electrode Locations to BESA/BEM Coordinates

Michael Boyle mrboyle at live.unc.edu
Thu Sep 17 16:56:21 PDT 2015

Hey James,

Thanks for your reply! I haven't seen too many researchers actually using
dipole fits to exclude components yet (just really method papers) so I feel
a little in the dark on some key points:

1. Fitting a single dipole vs. symmetric dipoles. I have adopted the
practice of fitting this model for all components and selecting the model
that has the lower Bayesian Information Criterion (with the inputs to BIC
being the residual variance and the number of parameters for the model (7
for the single dipole (6 dipole parameters plus the model noise term) and
10 for the 2-dipole model (since the second dipole only adds 3 degrees of
freedom since the x-y-z coordinates for both dipoles must be symmetric))),
but in reality the 2-dipole model will be the "ideal" (i.e. selected by
lower BIC) model more often than it should when visually looking at
component scalp maps. This is big because there are usually anywhere from a
few to more than 10 components that would be excluded in single dipole
model (due to either residual variance threshold or location outside the
head) that don't get excluded if the 2-dipole model is used and vice versa.
2. Selecting the variance threshold for component rejection. In all my fits
so far (this may be because of the poor coregistration of the EGI and BESA
coordinate systems), 15% residual variance threshold is way too low. I
would keep anywhere from 5% to 20% of components. I only get to the nominal
30% of components kept on average (I believe Makoto has said he experiences
this) if I set my residual variance threshold as high as 35%.

Any thoughts on these issues?

Also, I'm not sure how similar the Biosemi 128 channel electrode locations
are to the EGI 128 channel electrode locations, but I'll take a look at
that transformation matrix and see if it gives anything better than what I


On Thu, Sep 17, 2015 at 6:52 PM James Jones-Rounds <jj324 at cornell.edu>

> Hi Michael,
> I've had this problem in the past, too, using BioSemi's 128-channel
> system, which uses the ABCD montage (not 10-20). I had to do some manual
> warping, in the end, and I tried about a dozen set of parameters (x-, y-,
> and z-shift, pitch, roll and yaw, and radius changes in each dimension as
> well). For "pop_dipfit_settings", I use the standard MNI template brain
> image provided in EEGLAB's BEM folder, the BEM "standard_vol_SCCN.mat", and
> the "standard_alphabetic.elc" coordinate file, and these co-registration
> parameters:
> 'coord_transform', [0 -12  5  -0.1  0 -1.5708 97.88 92 97.8781]
> This both looks qualitatively like the electrodes are all on the scalp,
> and out of the dozen or so parameters I tried, is the one that maximizes
> the number of components with residual variances under 25%, which I take as
> a general sign of accuracy and good-fit. Nevertheless, most of my dipoles
> are always stuffed a bit further into the brain than I think is accurate
> (assuming that the cortex is what is primarily responsible for the EEG
> signal in the first place).
> I am soon going to be working on a project that has structural MR scans
> for each participant, which I hope will help improve the localization from
> the dipole-fitting process.
> Hope that helps!
> James
> On Thu, Sep 17, 2015 at 3:00 PM, <eeglablist-request at sccn.ucsd.edu> wrote:
>>    1. Registering EGI 128 Channel GSN Electrode Locations to
>>       BESA/BEM Coordinates (Michael Boyle)
>>    2. Re: Processing Startle in EEGlab (Tara Miskovich)
>> ---------- Forwarded message ----------
>> From: Michael Boyle <mrboyle at live.unc.edu>
>> To: EEGLAB Discussion Mailing List <eeglablist at sccn.ucsd.edu>
>> Cc:
>> Date: Wed, 16 Sep 2015 22:36:47 +0000
>> Subject: [Eeglablist] Registering EGI 128 Channel GSN Electrode Locations
>> to BESA/BEM Coordinates
>> Hey all,
>> I have been trying to get a good registration between the sensor
>> locations provided by EGI for their 128 channel geodesic sensor net and the
>> default BESA and BEM coordinate systems that DIPFIT provides, but the
>> results are quite unsatisfactory with the standard warping methods (no
>> manual warping). I have tried using the automatic warp when aligning just
>> the 10-20 sensor locations, the 10-10 sensor locations that EGI reports to
>> be within 1cm of an EGI GSN electrode (
>> ftp://ftp.egi.com/pub/documentation/technotes/HydroCelGSN_10-20.pdf),
>> both with and without fiducials, and even just assessing the correspondence
>> visually shows that the fits are quite poor. I was wondering if anyone has
>> had success getting a good registration particularly with the BESA
>> coordinates, since that is the dipole fitting method I've converged on. The
>> most noticeable issue with my registrations is with the frontal electrodes
>> in either model (the Fz's for example are clearly not well coregistered).
>> Possibly as a result, I have had, in a few cases, DIPFIT place the
>> well-fitting dipole for eye blink components slightly within the brain and
>> thus not automatically exclude them.
>> I can send pictures of my best attempts at registration to anyone
>> interested.
>> Thanks for your help!
>> Michael
>> --
> James Jones-Rounds
> Laboratory Manager
> Human Development EEG and Psychophysiology (HEP) Laboratory,
> Department of Human Development,
> --------------------------------------------
> Cornell University | Ithaca, NY
> 607-255-9883
> eeg at cornell.edu
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