[Eeglablist] Question: Montage and topoplots using MNE-python

Clement Lee cll008 at eng.ucsd.edu
Mon Sep 27 11:34:02 PDT 2021

Hi Golnoush,

Yes, I agree with your hunch that this is a coordinate system issue. The
two systems you are likely dealing with are the EEGLAB system (alias for
CTF) and the MNI system. You can try the montage files packaged with the
DIPFIT plug-in https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sccn_dipfit_tree_master_standard-5FBEM_elec&d=DwIBaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=xt7VBi6SbRhlsD5iNn1oYB79OaRoctkpWT88ZVjoHwA&s=ob1BVQgl1IMPzHaSGXrwiKdsIvUj48gAtW7r2RwO5CI&e= ,
where standard_1005.elc is in MNI coordsys and standard_1005_rotated.ced is
in the EEGLAB cordsys.

For more information, here is a short summary about the EEGLAB coordsys
situation: https://urldefense.proofpoint.com/v2/url?u=https-3A__eeglab.org_tutorials_ConceptsGuide_coordinateSystem.html&d=DwIBaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=xt7VBi6SbRhlsD5iNn1oYB79OaRoctkpWT88ZVjoHwA&s=0pSPi4VY1MlM0gFkCwO9Kirp8l-UPhTSg07BaFaF40s&e= 
and an in depth write up about different systems if you are interested:

Hope that helps,
Clement Lee
Applications Programmer
Swartz Center for Computational Neuroscience
Institute for Neural Computation, UC San Diego

On Fri, Sep 24, 2021 at 9:05 AM Alamian, Golnoush via eeglablist <
eeglablist at sccn.ucsd.edu> wrote:

> Hi there,
> I have built a pipeline to clean EEG datasets from different clinical
> sites, mainly using mne-python tools and functions. One issue that has come
> up a number of times is montage/electrode locations.
> For one dataset, when I use the ".loc" individual files from EEGlab as
> montage and try to plot the ICA components (as topoplots), I see that there
> is a clear rotation in the way the data is plotted. I have a feeling that
> this might be a compatibility issue between the way mne-python deciphers
> electrode coordinates and the coordinates obtained through individual
> ".loc" via EEGlab.
> Has anyone else encountered this issue? I have attached a screenshot of
> ICA components as topoplots and as a time-series, where it is clear that
> components 0 and 2 are ocular artefact that are plotted 270degrees from the
> centre (rotated 90 degrees to the left).
> Any insight would be appreciated.
> Thank you!
> Golnoush
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