[Eeglablist] Version 2026 bug? Unable to rereference to the average reference and add back online ref
Cedric Cannard
ccannard at protonmail.com
Tue Jun 30 10:44:18 PDT 2026
Hi Mate and all,
Here is how I do it with a custom function I made:
1. Load your data
2. Load your channel locations
e.g.:
dipfitDir = fileparts(which('pop_dipfit_settings'));
EEG2 = pop_chanedit(EEG2, {'lookup', ...
fullfile(dipfitDir, 'standard_BEM', 'elec', 'standard_1005.elc')});
3. Copy structure dataset with locations for interpolation
oriEEG = EEG;
4. Remove bad channels
5. Clean artifacts
6. Interpolate bad channels
EEG = pop_interp(EEG, oriEEG.chanlocs, 'spherical');
7. Re-reference, adding back the reference channels (EDIT LABELS WITH YOUR REFERENCE LABEL)
EEG = apply_car(EEG, {'FCz' 'AFz'}, oriEEG.chanlocs); % add path to the below function first (or insert as local helper at the bottom of your script)
8. If running ICA, make sure to calculate the rank with:
C = cov(double(EEG.data'));
eigVals = eig(C);
dataRank = sum(eigVals > 1e-7 * max(eigVals)); % relative threshold
fprintf(' ICA rank: %d\n', dataRank)
EEG = pop_runica(EEG, 'icatype','runica', 'options', {'extended', 1, 'pca', dataRank});
function EEG = apply_car(EEG, refLabels, chanlocs_template)
% apply_car - Full-rank common average reference (CAR)
%
% Optionally recovers online reference channel(s) by adding them with proper
% locations and interpolating them before CAR. A zero-filled dummy channel
% is always added for rank preservation during CAR and removed afterward.
%
% EEG = apply_car(EEG)
% EEG = apply_car(EEG, refLabels, chanlocs_template)
%
% Inputs:
% EEG - EEGLAB EEG struct
% refLabels - string or cell array of reference label(s) to recover
% chanlocs_template - chanlocs struct or path to electrode file (used as
% fallback; BEM standard_1005.elc is primary source).
%
% Outputs:
% EEG - re-referenced EEG struct. Reference channel(s) are interpolated
% and retained before CAR is applied.
%
% Usage:
% EEG = apply_car(EEG);
% EEG = apply_car(EEG, {'FCz','AFz'}, oriEEG.chanlocs);
%
% References:
% Makoto's preprocessing pipeline: https://eeglab.ucsd.edu/wiki/Makoto's_preprocessing_pipeline
% Kim et al. (2023). ICA's bug. Front. Signal Process., 3, 1064138.
rankBefore = sum(eig(cov(double(EEG.data'))) > 1e-7);
fprintf('apply_car: rank before CAR = %d / %d\n', rankBefore, EEG.nbchan);
retainRefs = nargin == 3 && ~isempty(refLabels) && ~isempty(chanlocs_template);
if retainRefs
if ischar(refLabels) || isstring(refLabels)
refLabels = cellstr(refLabels);
end
refLabels = refLabels(~ismember(refLabels, {EEG.chanlocs.labels}));
newChanIdx = zeros(1, numel(refLabels));
% Add zero-filled channels with placeholder chanlocs
for i = 1:numel(refLabels)
EEG.data(end+1, :) = 0;
EEG.nbchan = EEG.nbchan + 1;
EEG.chanlocs(end+1) = EEG.chanlocs(1); % temp placeholder, overwritten below
EEG.chanlocs(end).labels = refLabels{i};
newChanIdx(i) = EEG.nbchan;
end
% Look up correct locations using pop_chanedit with BEM template
% This handles all coordinate conversions (XYZ -> theta/radius/etc.)
bemPath = which('standard_1005.elc');
if isempty(bemPath)
error('apply_car: standard_1005.elc not found. Ensure EEGLAB dipfit plugin is installed.');
end
EEG = pop_chanedit(EEG, 'lookup', bemPath);
% Interpolate the newly added zero-filled channels
EEG.data = double(EEG.data);
EEG = eeg_checkset(EEG);
EEG = pop_interp(EEG, newChanIdx, 'spherical');
end
% Always add dummy zero row for rank preservation, apply CAR, remove dummy
EEG.data(end+1, :) = 0;
EEG.nbchan = EEG.nbchan + 1;
EEG.data = EEG.data - mean(EEG.data, 1);
EEG.data(end, :) = [];
EEG.nbchan = EEG.nbchan - 1;
rankAfter = sum(eig(cov(double(EEG.data'))) > 1e-7);
fprintf('apply_car: rank after CAR = %d / %d\n', rankAfter, EEG.nbchan);
EEG = eeg_checkset(EEG);
end
Hope this helps,
Cedric
Sent with Proton Mail secure email.
On Tuesday, June 30th, 2026 at 9:46 AM, Gyurkovics, Mate via eeglablist <eeglablist at sccn.ucsd.edu> wrote:
> Hi Arno et al.,
>
> I am grappling with something similar so I thought I'd piggyback on this thread if that's okay.
>
> I have a 32-channel recording that was referenced to Cz online. I am trying to add back Cz and then re-referencing to the average. My problems start even before the re-referencing step.
>
> I tried the following line of code to add Cz:
>
> EEG=pop_chanedit(EEG, 'append',31,'changefield',{32,'labels','Cz'},'changefield',{32,'theta','0'},'changefield',{32,'radius','0'},'convert',{'topo2all'});
>
> Not only does this not add a 32nd channel, it changes all the other channels - in EEG.chanlocs, they now all have the label 'E', and the coordinates are off too. I played around a bit with the code and it seems like the issue is the topo2all conversion. Unfortunately, this is the only coordinate info for Cz for our montage that I have from collaborators at the moment, so I cannot manually specify anything beyond the theta and the radius.
>
> I did try the GUI (Edit > Channel locations) as well which does give me other values once I put in theta and radius, but it also messes up the other channels in the same way. So I just took the values output by the GUI, and created a brute force way of adding Cz.
>
> EEG.data(32,:) = repelem(0,size(EEG.data,2));
> EEG.nbchan = size(EEG.data,1);
> EEG.chanlocs(EEG.nbchan).labels = 'Cz';
> EEG.chanlocs(EEG.nbchan).sph_phi = 90; EEG.chanlocs(EEG.nbchan).sph_theta = 0;
> EEG.chanlocs(EEG.nbchan).theta = 0; EEG.chanlocs(EEG.nbchan).radius = 0;
> EEG.chanlocs(EEG.nbchan).X = 5.5307e-17; EEG.chanlocs(EEG.nbchan).Y = 0; EEG.chanlocs(EEG.nbchan).Z = 0.90323;
>
> This does work, but I'm worried it's not updating every bit of metadata that it should.
>
> Is this piece of code okay? If I do this and then average reference, everything looks as expected (i.e., Cz is no longer flat).
>
> Thanks,
> Mate
>
> ________________________________
> Feladó: eeglablist <eeglablist-bounces at sccn.ucsd.edu>, meghatalmazó: Arnaud Delorme via eeglablist <eeglablist at sccn.ucsd.edu>
> Elküldve: 2026. június 27., szombat 3:40
> Másolatot kap: eeglab list <eeglablist at sccn.ucsd.edu>
> Tárgy: Re: [Eeglablist] Version 2026 bug? Unable to rereference to the average reference and add back online ref
>
> The issue is that
>
> EEG = pop_reref( EEG, [], 'refloc', struct('labels',{'Cz'}, 'type',{'eeg'}, 'theta',177.4959, 'radius',0.029055, 'X',-9.167, 'Y',-0.4009, 'Z',100.244, 'sph_theta',-177.4959, 'sph_phi',84.77, 'sph_radius',100.6631, 'urchan',EEG.nbchan+1, 'ref',{''}, 'datachan',0) );
>
> Is adding a second channel Cz. If you already have a channel Cz and it does not have coordinates, you should add them instead in the channel editor (or from the command line using pop_chanedit). This is detailed in that page.
>
> https://urldefense.com/v3/__https://eeglab.org/tutorials/05_Preprocess/rereferencing.html__;!!Mih3wA!FzwrfBmBPxLmdJ_Fasn-abQBAUGHpBk41qiqMFzw20WDRK_0wJutkbz3EN7zqsBdDxfK53TfMmd0QWF1HppIzz_d$
>
> Best wishes,
>
> Arno
>
> > On Jun 17, 2026, at 08:37, Miller, Carol Anne via eeglablist <eeglablist at sccn.ucsd.edu> wrote:
> >
> > I have encountered a problem similar to what Kelsey and Andrew described (prior to their posts). I was wondering if there have been any updates, like is it really a bug and if so has it been fixed? Using Windows, EEGLAB 2025, Matlab 2024a.
> > Full disclosure: I have not yet tried Andrew's workaround but am hoping I won't have to!
> >
> > Thanks,
> > Carol
> >
> >
> > Carol A. Miller, Ph.D.
> >
> > Professor of Communication Sciences and Disorders and Linguistics
> >
> > 404K Ford Building
> >
> > 498 Allen Road
> >
> > University Park, PA 16802
> >
> > cam47 at psu.edu
> >
> > Pronouns: she/her
> >
> > My work day may look different than your work day. Please do not feel any pressure to respond out of your normal working hours.
> >
> > ________________________________
> > From: eeglablist <eeglablist-bounces at sccn.ucsd.edu> on behalf of Andrew Corcoran via eeglablist <eeglablist at sccn.ucsd.edu>
> > Sent: Tuesday, May 19, 2026 5:14 AM
> > To: eeglablist at sccn.ucsd.edu <eeglablist at sccn.ucsd.edu>
> > Subject: [Eeglablist] Version 2026 bug? Unable to rereference to the average reference and add back online ref
> >
> > I recently experienced a similar problem to Kelsey when trying to adapt some old code for new BioSemi data using EEGLAB 2026 in MATLAB 2025a.
> >
> > With some playing around via the gui I managed to get things working as follows :
> >
> > % import chanlocs & define chantype
> > EEG = pop_chanedit(EEG, {'lookup','standard_1005.elc'});
> >
> > % assign ref
> > EEG = pop_reref( EEG, [ contains({EEG.chanlocs.labels}, {'Cz'} ) ] );
> >
> > % reintroduce Cz & reref to common average
> > EEG = pop_chanedit(EEG, 'append', EEG.nbchan, 'changefield', {EEG.nbchan+1,'labels','Cz'}, ...
> > 'lookup', 'standard_1005.elc');
> >
> > EEG = pop_reref( EEG, [], 'refloc', struct('labels',{'Cz'}, 'type',{'eeg'}, ...
> > 'theta',177.4959, 'radius',0.029055, 'X',-9.167, 'Y',-0.4009, 'Z',100.244, ...
> > 'sph_theta',-177.4959, 'sph_phi',84.77, 'sph_radius',100.6631, 'urchan',EEG.nbchan+1, ...
> > 'ref',{''}, 'datachan',0) );
> >
> > While this code appears to function as intended, running it produces the following warning :
> > Warning: some channels have the same label
> >
> > I cannot see any evidence of incorrect labelling despite the warning. Whatever the source of the issue, it appears to be the same problem as previously raised on this list by Raquel London https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fsccn.ucsd.edu*2Fpipermail*2Feeglablist*2F2016*2F011065.html&data=05*7C02*7Ccam47*40psu.edu*7C925cf2493b44435f40b108deb59e7799*7C7cf48d453ddb4389a9c1c115526eb52e*7C0*7C0*7C639147889381256261*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C&sdata=dULJSVZlLGdsKJAWuaDiKUo40ZGZ2qMYOBRT9rZugks*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!BKijivb65F94Fh3pakg9Ea433tP9cJtHZ8YhJahPfm_O_VMmOZ2TiTTMrpByWciehp1wSuW1rY3ZBfQjSWE$ <https://urldefense.com/v3/__https://sccn.ucsd.edu/pipermail/eeglablist/2016/011065.html__;!!DZ3fjg!8PqS8j_EaZMwIRUJIrCS4cNG4BCu9OBUvTRkq9XOOg17YN2nlYdIjas9HAs68DLEeiSqyOdGq6YEyqCe_stE_Du_PcQ$ > (I’m not sure if anyone got to the bottom of it).
> >
> > Venlig hilsen
> > Andrew
> >
> > Dr. Andrew W. Corcoran
> > Postdoctoral Researcher
> >
> > Københavns Universitet
> > Institut for Idræt og Ernæring<https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fnexs.ku.dk*2F__*3B!!Mih3wA!CpsvdSQpAQtDgps7UcdHM6iIBWQoB77bprwNjhp1wo1SFvi8cNP0jI6p3Iqrle4fkR5Y6wFkqPX4w0blhx8-4g*24&data=05*7C02*7Ccam47*40psu.edu*7C925cf2493b44435f40b108deb59e7799*7C7cf48d453ddb4389a9c1c115526eb52e*7C0*7C0*7C639147889381286684*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C&sdata=j9UJTHx1YLw4rDJQAFYZkyjyUZJ*2F1bep7sh*2Batgve34*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!BKijivb65F94Fh3pakg9Ea433tP9cJtHZ8YhJahPfm_O_VMmOZ2TiTTMrpByWciehp1wSuW1rY3ZGofja5A$ >
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