[Eeglablist] Order of Channel Removal+Interpolation and ICA (removing noisy components)

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Mon Jun 1 17:59:00 PDT 2026 

Hi Naviya,

1. Should I use script to first save the number of the channels, then
remove the noisy ones and then interpolate the ones removed


Yes, at least that's what I do. ASR needs to be applied after excluding bad
channels. Re-reference to average potential and ICA (arguably) need to be
done after channel interpolation.

2. If I interpolate the noisy channels without removing them


How can you?

n_chans = EEG.nbchan; data_rank = rank(double(EEG.data(:,:))); % or just:
n_chans - n_interpolated
EEG = pop_runica(EEG, 'icatype', 'runica', 'extended', 1, 'pca', data_rank);


Actually, as long as ICA can assign a single component to a single bad
channel, including or excluding a bad channel for ICA does not matter, at
least in theory. However, in reality, removing bad channels before ICA is
probably safer.

3. Dr. Miyakoshi- If I follow this strategy of interpolating before ICA,
would it be sensible to cite the paper you referred to?- Kim H, Luo J, Chu
S, Cannard C, Hoffmann S and Miyakoshi M (2023) ICA’s bug: How ghost ICs
emerge from effective rank deficiency caused by EEG electrode interpolation
and incorrect re-referencing. Front. Sig. Proc. 3:1064138. doi:
10.3389/frsip.2023.1064138


If you run Hoffmann's test, namely min(eig(cov(EEG.data')))> 1E-6 to check
'effective rank deficiency' before ICA, then yes, you may want to cite the
ICA's bug paper to give him a credit. There were multiple hidden agenda in
that paper, and giving him credit for his finding was one of them.

Makoto

On Fri, May 29, 2026 at 2:52 AM Naviya Lall <naviyal at iiitd.ac.in> wrote:

> Thank you for these responses, they are incredibly helpful. Brief follow
> up questions-
> 1. Should I use script to first save the number of the channels, then
> remove the noisy ones and then interpolate the ones removed *OR* can I
> just tell EEGLAB the noisy channels and then interpolate without removing
> like this:
> bad_idx = find(ismember({EEG.chanlocs.labels}, {'F10'}));  %
> EEG = pop_interp(EEG, bad_idx, 'spherical');
> EEG = eeg_checkset(EEG);
> [ALLEEG, EEG, CURRENTSET] = eeg_store(ALLEEG, EEG, CURRENTSET);
>
> 2. If I interpolate the noisy channels without removing them, do I still
> run the PCA adjusted ICA? like so-
> n_chans = EEG.nbchan; data_rank = rank(double(EEG.data(:,:))); % or just:
> n_chans - n_interpolated
> EEG = pop_runica(EEG, 'icatype', 'runica', 'extended', 1, 'pca',
> data_rank);
>
> 3. Dr. Miyakoshi- If I follow this strategy of interpolating before ICA,
> would it be sensible to cite the paper you referred to?- Kim H, Luo J, Chu
> S, Cannard C, Hoffmann S and Miyakoshi M (2023) ICA’s bug: How ghost ICs
> emerge from effective rank deficiency caused by EEG electrode interpolation
> and incorrect re-referencing. Front. Sig. Proc. 3:1064138. doi:
> 10.3389/frsip.2023.1064138
>
> Thank you!
>
> Best regards,
> Naviya
>
> --
> Naviya Lall
> Junior Research Fellow
> Cognitive Science Lab
> IIIT Delhi
> naviyalalluni.wixsite.com
> <https://urldefense.com/v3/__https://naviyalalluni.wixsite.com/naviyalall__;!!Mih3wA!BgUshfFRwA_jdbzWt1Wl7e-UyW0RxRqTHK3MnBWuS1uLxQcGEzG9uIgmMyHrIzz0it5rMtI9AL6WsyYJCREs-w$>
>
>
> On Fri, May 29, 2026 at 3:18 AM Makoto Miyakoshi via eeglablist <
> eeglablist at sccn.ucsd.edu> wrote:
>
>> Hi Marshid and Tim,
>>
>> Thank you for your comments. It's my honor to go against Claude's advice!
>>
>> In fact, I recognize Claude's workaround works fine for a specific
>> purpose:
>> it uses ICA purely as an electrode signal cleaner at the cost of
>> IC-electrode correspondence i.e., your EEG.icawinv will be invalidated. As
>> a result, certain types of analyses become impossible, such as
>> envelope-topography (envtopo) at the group-level analysis, because matrix
>> dimensions do not match across datasets.
>>
>> Here is the step by step examination.
>>
>> 1. We all agree that bad channels need to be excluded before ICA. Suppose
>> that we reject n channels here.
>>
>> 2. We run ICA on this channel-reduced data. As a result, the reduced
>> number
>> of electrodes are registered to your ICA-generated matrices
>> (EEG.icaweights, EEG.icasphere, EEG.icawinv, EEG.chaninds).
>>
>> 3. After ICA, you interpolate rejected channels to recover your original
>> EEG.nbchan. Technically, you can do it. Probably you see no error message
>> in EEGLAB. However, this interpolation does not take care of ICA-generated
>> matrices (as far as I know). As a result, you can't perform IC rejection
>> for electrode signal cleaning because the number of channels of your scalp
>> recording and of your ICA-generated matrices do not match. You do see an
>> error message here.
>>
>> 4. The easiest way (i.e., without developing a reasonable workaround and
>> publishing it a dedicated technical paper to address this specific
>> problem)
>> to avoid this problem is to perform channel interpolation BEFORE ICA so
>> that all the original electrodes are registered to ICA-generated matrices
>> so that you can perform IC rejection etc. after ICA. The drawback is that
>> you need to use PCA (or whatever) dimension reduction to run full-rank ICA
>> decomposition: see my ICA's bug paper for detail. Spline channel
>> interpolation is the most dangerous process for ICA because it does not
>> cause a clean rank deficiency due to its nonlinearity. If the smallest
>> eigenvalue is < 1E-6, ICA starts to generate 'ghost ICs', even though
>> Matlab's rank() function says 'the data are full ranked'! I credit Sven
>> Hoffmann for finding this threshold.
>>
>> To conclude, my suggestion guarantees group-level data compatibility
>> between scalp and IC sources at the cost of the use of PCA dimension
>> reduction in ICA, and Claude's suggestion works fine only for channel data
>> analysis.
>>
>> Makoto
>>
>> On Thu, May 28, 2026 at 9:24 AM Tim Curran <tim.curran at colorado.edu>
>> wrote:
>>
>> > Hi Makoto,
>> > I have been playing with Claude Code, and using the latest Claude.md
>> file
>> > with EEGLAB.
>> >
>> > Claude.md file says:
>> > "Typical pipeline position: clean_rawdata (removes bad channels) ->
>> > re-reference -> ICA -> ICLabel -> remove components -> **interpolate**
>> ->
>> > re-reference (again, optional) -> epoch.”
>> >
>> > You do not agree with eeglab’s Claude.md file or maybe I am missing
>> > something?
>> >
>> > thanks
>> > Tim
>> >
>> >
>> >
>> > *From: *eeglablist <eeglablist-bounces at sccn.ucsd.edu> on behalf of
>> Makoto
>> > Miyakoshi via eeglablist <eeglablist at sccn.ucsd.edu>
>> > *Date: *Wednesday, May 27, 2026 at 5:41 PM
>> > *To: *eeglablist at sccn.ucsd.edu <eeglablist at sccn.ucsd.edu>
>> > *Subject: *Re: [Eeglablist] Order of Channel Removal+Interpolation and
>> > ICA (removing noisy components)
>> >
>> > [External email - use caution]
>> >
>> >
>> > Hi Naviya,
>> >
>> >    - My main question is if I should perform interpolation before ICA
>> > or after ICA?
>> >
>> > Do it BEFORE ICA.
>> > If you perform channel interpolation after ICA, your EEG.icasphere does
>> not
>> > have columns for the added channel.
>> >
>> > Makoto
>> >
>> > On Tue, May 26, 2026 at 2:19 PM Naviya Lall via eeglablist <
>> > eeglablist at sccn.ucsd.edu> wrote:
>> >
>> > > Hello all,
>> > >
>> > > My name is Naviya and I work with EEG data in a lab in Delhi, India. I
>> > have
>> > > a question about EEG data channel interpolation and its order in
>> > > preprocessing pipelines.
>> > >
>> > >    - We record data with high density EEG (128 channels).
>> > >    - I tried to perform ICA without removing any channels and it was
>> > giving
>> > >    me noise heavy components (I use ICA to remove noisy components of
>> > eye,
>> > >    heart, muscle etc.)
>> > >    - I just want to remove 2-4 channels in some participants or
>> certain
>> > >    sessions.
>> > >    - The GUI has very easy direct interpolation
>> > >    steps- Tools>Interpolate>select from data channels which skips the
>> > >    "Removal" step altogether.
>> > >    - In code I feel that it would be easier to "remove" the noisy
>> > >    channel(s) and use this -  original_chanlocs = EEG.chanlocs; (to
>> save
>> > >    original locations) and then  EEG = pop_interp(EEG,
>> original_chanlocs,
>> > >    'spherical');
>> > >    to interpolate the removed data- *Is that right?*
>> > >    - My main question is if I should perform interpolation before ICA
>> or
>> > >    after ICA?
>> > >    - I read through some older exchanges on EEGLABLIST Archive from
>> 2015,
>> > >    2017, 2023 and 2025 however I am still unsure of the ideal order of
>> > >    performing interpolation.
>> > >    - My logical thought is to remove + interpolate before running ICA
>> so
>> > >    that the rank and number of components generated is not affected
>> but
>> > > most
>> > >    people advise to remove channel, then ICA and then interpolate.
>> > >    - Please advise on the method of channel removal+interpolation and
>> the
>> > >    order of channel interpolation and ICA?
>> > >
>> > >
>> > > Thank you so much.
>> > >
>> > >
>> > > Best regards,
>> > > Naviya
>> > >
>> > > --
>> > > Naviya Lall
>> > > Junior Research Fellow
>> > > Cognitive Science Lab
>> > > IIIT Delhi
>> > > naviyalalluni.wixsite.com
>> <https://urldefense.com/v3/__http://naviyalalluni.wixsite.com__;!!Mih3wA!BgUshfFRwA_jdbzWt1Wl7e-UyW0RxRqTHK3MnBWuS1uLxQcGEzG9uIgmMyHrIzz0it5rMtI9AL6WsyafPUEjKQ$>
>> <
>> > >
>> >
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