[Eeglablist] Order of Channel Removal+Interpolation and ICA (removing noisy components)
m za
ma.zamani.20 at gmail.com
Wed Jun 3 12:19:28 PDT 2026
Hi all,
I work with low-density EEG recordings (typically 19 channels, and in some
datasets even fewer) and am interested in effective connectivity analysis
(e.g., DTF, PDC, and Granger causality).
My original goal was to perform connectivity analysis at the source level.
However, in practice I encountered a number of methodological and technical
difficulties with source reconstruction pipelines. Given the low electrode
density and various practical issues with the available workflows, I
eventually moved to a channel-level approach in order to keep the analysis
feasible.
A related challenge is that some recordings contain bad channels that need
to be rejected. In high-density EEG, channel interpolation is often a
reasonable solution. However, with low-density recordings (e.g., 14–19
channels), removing only a few channels may represent a substantial
fraction of the montage, and I am not always convinced that channel
interpolation is an ideal solution in this situation. As a result, the
effective number of channels may vary across participants.
For these reasons, I currently construct broad ROIs by averaging groups of
electrodes and then estimate effective connectivity between the resulting
ROI signals.
Recently, after reading discussions on the EEGLAB list about ICA-derived
components as "effective sources," I started wondering whether ICA-based
approaches might provide a more meaningful representation of brain dynamics
than conventional channel-based ROIs for low-density EEG.
My question is therefore not about source localization itself. Rather, I am
trying to determine which of the following practical approaches would be
more appropriate:
1. Channel-based ROI connectivity:
Channels → ROI signals → Effective connectivity
2. ICA-based connectivity:
ICA → Brain ICs → Effective connectivity
If the ICA-based approach is preferable, I am also uncertain about the most
appropriate way to incorporate ROIs.
Would it be better to:
A) First group brain-related ICs into broad cortical regions (based on
scalp maps and/or dipole locations when available), construct regional
signals from the IC activations, and then estimate effective connectivity
between those regional signals?
or
B) First estimate effective connectivity between the brain ICs themselves,
and only afterwards summarize or aggregate the resulting connectivity
measures at the regional level?
A related concern is how correspondence between ICs should be established
across participants. Since ICA decomposition produces different numbers and
types of ICs for different individuals, assigning ICs to common ROIs is not
straightforward.
For group-level analyses, would manual assignment of brain ICs to broad
ROIs based on scalp topographies be considered acceptable, or would some
form of IC clustering (e.g., based on scalp maps, spectra, and/or dipole
information) generally be preferred?
More generally, for low-density EEG recordings where source reconstruction
is not a practical option and channel interpolation may also be
problematic, is there a methodological advantage in using ICA-derived brain
components instead of conventional channel-based ROIs when estimating
effective connectivity?
I would greatly appreciate any recommendations, practical experiences, or
references related to this issue.
Thank you very much.
On Wed, 3 Jun 2026, 17:51 Scott Makeig via eeglablist, <
eeglablist at sccn.ucsd.edu> wrote:
> A simpler and more biologically correct approach is to reject 'bad'
> channels (e.g., those NOT containing EEG in all or some part), then perform
> ICA decomposition.
>
> Then, perform analysis only at the level of ICs. Interpolate only the IC
> scalp projection maps -- for plotting and for comparing across participants
> (e.g. IC clustering).
>
> Why? Because each EEG channel (say, Cz-REF) IS a spatial filter summing
> potentials arising in some large portion of cortex - some portion not
> within any one functional area. Thus, scalp channels are poor spatial
> filters. If the goal is to record/study/use brain electrical activity
> (dominated, in scalp recordings, by cortical projections plus non-brain
> artifacts from eyes, etc.), then ICA decomposition provides derived
> 'channels' that are better spatial filters, i.e. filtering to maximize
> collection of one distinct brain signal while rejecting other distinct
> signals from other source areas.
>
> I have long referred to ICs compatible with cortical activity as 'effective
> sources' - since we cannot identify the boundaries of the cortical
> generator region. However, in many favorable cases, one can at least
> localize the effective 'center' of the region using a one (or sometimes
> two) equivalent dipole model - accurate to the extent that the electrical
> model of the head (geometry and tissue conductances) used in computing the
> model conforms to the head of the participant.
>
> Note: In practice, equivalent dipole localization is least accurate in its
> depth dimension (see Akalin Acar 2013). This is because individual skull
> conductance values vary widely, and there is no widely used (and, e.g.,
> non-invasive!) method for ascertaining this for individual participants
> (other than the SCALE method introduced by Zeynep Akalin Acar and me in
> 2016).
>
> But in non-radial dimensions, equivalent dipole localization is quite
> accurate. This is proven by the replicability of equivalent dipole
> positions for clusters of ICs capturing, e.g., somatomotor hand area mu
> rhythms. Because of individual differences in physical brain geometry not
> captured in any template head model, plus normal functional brain geometry
> differences, such clusters cannot be expected to be infinitely tight. But
> in our research they have proven to be remarkably tight.
>
> In sum - I see the primary myth in the minds of many or most EEG
> researchers to be that the raw scalp channel data is/are 'THE' data -
> i.e., THE 'true' representation of the recorded data. This is like
> believing that the number 12 *is REALLY* 12x1 and *is NOT really* 3x4 ...
> Whereas, actually, the number 12 is equally both - it depends on the way
> you (construct, deconstruct, look at) it.
>
> EEG data is just a set of electrical time series data channels recording
> the output of simple spatial filters -- each recording the potential
> difference between two (or more) points on the scalp. What they are
> recording is the temporally and geometrically highly complex brain activity
> (dominated by radial potential gradients emanating from every mm^2 of
> cortex - plus non-brain 'artifact' sources, summed in the recording
> channels).
>
> The EEG channel signals themselves are NOT the TRUE signals emanating from
> the cortex (plus artifact) - any more than directional microphones set up
> in various places around a park perfectly capture individual voices,
> individual songbirds, etc. in the busy park). Our brains are highly tuned
> to audio signal separation and recognition -- but this is the result of
> highly complex brain signal processing, as evidenced first of all by the
> physiological complexity of the auditory system (inner ear-to-neural
> impulse complexities, multiple ascending brainstem way stations, multiple
> cortical representations, etc.).
>
> We don't simply 'hear' each ear's 'single audio track' !
>
> For EEG, we need to provide all this signal analysis ourselves, as we have
> no 'ascending brainstem' machinery to sort things out for us... The best we
> have, at present, is ICA decomposition into effective source signals, which
> can then in turn be studied for their relationships to sensory, motor,
> emotional, and other events -- and to each other.
>
> The raw scalp channel records are not, individually, the form of 'the' EEG
> data that is most useful for studying the recorded brain dynamics...
>
> Scott
>
> On Tue, Jun 2, 2026 at 12:20 AM Makoto Miyakoshi via eeglablist <
> eeglablist at sccn.ucsd.edu> wrote:
>
> > Hi Jason,
> >
> > EEG.data = EEG.icawinv then run interpolation? Ok you won. I never
> thought
> > of that approach.
> >
> > That said, I take Fiorenzo's PCA-ICA paper differently. The message of
> the
> > paper is for users who aggressively reduce dimensions, like those in
> early
> > Hivarynen's group who reduced data rank until IC subspace never appears.
> In
> > my suggested process, I drop a few dimensions to data full rank, which is
> > not what Fiorenzo tested in that paper.
> >
> > EEGLAB's default channel interpolation uses spherical spline
> interpolation
> > (Perrin et al., 1989) which is why clean rank deficiency does not happen.
> > Instead, it adds a ghost dimension of min(eng(cov(EEG.data'))) < 1E-6.
> This
> > way, ICA is forced to solve an undercomplete problem, and 'ghost ICs'
> > appear as a result.
> >
> > Makoto
> >
> > On Mon, Jun 1, 2026 at 7:46 PM Jason Palmer <japalmer29 at gmail.com>
> wrote:
> >
> > > I made an eeglab function (shown below) to do the post ica channel
> > > interpolation for anyone interested. I tested it and it seems to work.
> > >
> > > -Jason
> > >
> > > function EEGout = eeg_icainterp(EEG,urchanlocs)
> > > % function EEGout = eeg_icainterp(EEG,urchanlocs)
> > > %
> > > % Interpolate missing channels of EEG.icawinv (ICA maps) and EEG data
> > > %
> > > % Inputs:
> > > %
> > > % EEG - a dataset with ICA from data with
> rejected /
> > > missing channels
> > > % urchanlocs - array of channel locations with missing
> channels
> > > %
> > > % Outputs:
> > > %
> > > % EEGout - dataset with ICA maps and data with rejcted /
> > > % missing channels interpolated
> > > %
> > >
> > > % get the original channel numbers
> > > for k = 1:EEG.nbchan
> > > v(k) = EEG.chanlocs(k).urchan;
> > > end
> > >
> > > % create fake dataset to interpolate ica maps
> > > EEGtmp = EEG;
> > > EEGtmp.data = EEGtmp.icawinv;
> > > EEGtmp.trials = 1;
> > > EEGtmp.pnts = size(EEGtmp.icawinv,2);
> > > EEGtmp2 = eeg_interp(EEGtmp,urchanlocs);
> > >
> > > % copy the icaact and interpolated icawinv into output
> > > EEGout = EEG;
> > > EEGout.nbchan = length(urchanlocs);
> > > EEGout.icawinv = EEGtmp2.data;
> > > EEGout.icaact = EEG.icaact;
> > >
> > > % add zero columns to icasphere where (new) interpolated data channels
> > are
> > > EEGout.icasphere(:,v) = EEG.icasphere;
> > > EEGout.icasphere(:,setdiff(1:EEGout.nbchan,v)) = 0;
> > >
> > > % add data with interpolated channels
> > > EEGout.data = reshape(EEGout.icawinv *
> > > double(EEGout.icaact(:,:)),EEGout.nbchan,EEGout.pnts,EEGout.trials);
> > >
> > > % copy full chanlocs and icachansind
> > > EEGout.chanlocs = urchanlocs;
> > > EEGout.icachansind = 1:EEGout.nbchan;
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: japalmer29 at gmail.com <japalmer29 at gmail.com>
> > > Sent: Saturday, May 30, 2026 9:51 PM
> > > To: 'Tim Curran' <tim.curran at colorado.edu>; 'Naviya Lall' <
> > > naviyal at iiitd.ac.in>; 'Makoto Miyakoshi' <mmiyakoshi at ucsd.edu>
> > > Cc: eeglablist at sccn.ucsd.edu
> > > Subject: RE: [Eeglablist] Order of Channel Removal+Interpolation and
> ICA
> > > (removing noisy components)
> > >
> > > I forgot the final step:
> > >
> > > 8. Replace EEG.data in the ica dataset with the interpolated
> EEG.icawinv
> > *
> > > EEG.icaact
> > >
> > > Jason
> > >
> > > -----Original Message-----
> > > From: japalmer29 at gmail.com <japalmer29 at gmail.com>
> > > Sent: Saturday, May 30, 2026 9:40 PM
> > > To: 'Tim Curran' <tim.curran at colorado.edu>; 'Naviya Lall' <
> > > naviyal at iiitd.ac.in>; 'Makoto Miyakoshi' <mmiyakoshi at ucsd.edu>
> > > Cc: eeglablist at sccn.ucsd.edu
> > > Subject: RE: [Eeglablist] Order of Channel Removal+Interpolation and
> ICA
> > > (removing noisy components)
> > >
> > > Hi all,
> > >
> > > It seems that a major concern here is to keep all the channel locations
> > in
> > > the dataset. However, I think this is possible without interpolating
> > first.
> > >
> > > Since spherical interpolation is just a linear combination of
> neighboring
> > > channels, the resulting dataset will be rank deficient, and ICA should
> > > remove the redundant dimensions by PCA. PCA reduction has been shown to
> > be
> > > detrimental by Artoni.
> > >
> > > Alternatively, you can interpolate the component maps of the mixing
> > > matrix. However, as there is no function currently to do this, the
> > process
> > > is a bit roundabout. I and a colleague in Germany have done this
> > > successfully in the past.
> > >
> > > The process is:
> > >
> > > 1. Save the full channel locations
> > > 2. Reject bad channels
> > > 3. Run ICA
> > > 4. Create fake dataset with the EEG.icawinv as EEG.data, adding
> back
> > > in zero rows for the rejected channels with the original channel
> > locations
> > > 5. Run eeg_interp on the fake dataset to get full icawinv
> > > 6. Copy full icawinv and full channel locations into the ica
> dataset
> > > 7. Add zero columns to the icasphere matrix corresponding to the
> bad
> > > channels.
> > >
> > > Best,
> > > Jason
> > >
> > > -----Original Message-----
> > > From: eeglablist <eeglablist-bounces at sccn.ucsd.edu> On Behalf Of Tim
> > > Curran via eeglablist
> > > Sent: Friday, May 29, 2026 2:50 PM
> > > To: Naviya Lall <naviyal at iiitd.ac.in>; Makoto Miyakoshi <
> > > mmiyakoshi at ucsd.edu>
> > > Cc: eeglablist at sccn.ucsd.edu
> > > Subject: Re: [Eeglablist] Order of Channel Removal+Interpolation and
> ICA
> > > (removing noisy components)
> > >
> > > Thanks for the replies. Very helpful!
> > > best
> > > Tim
> > >
> > >
> > > From: eeglablist <eeglablist-bounces at sccn.ucsd.edu> on behalf of
> Naviya
> > > Lall via eeglablist <eeglablist at sccn.ucsd.edu>
> > > Date: Friday, May 29, 2026 at 10:25 AM
> > > To: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> > > Cc: 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]
> > >
> > >
> > > 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://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fnaviyalalluni.wixsite.com*2Fnaviyalall__*3B!!Mih3wA!FQyTrO4VCQzKiAaHQYBhwg-G7LrmGyGdl2DOVzeIYwL4krOhTWwF7h59XTGli76LuO9fipK7WDEdwyD-E89CpGG1*24&data=05*7C02*7Ctim.curran*40colorado.edu*7C1beb1b4b14744df80a1408debd9ee86a*7C3ded8b1b070d462982e4c0b019f46057*7C1*7C0*7C639156687403992007*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C&sdata=DEhskU0UGYxm4gtRt1NWvwbHYYOBzFSsvCxepjcfsyg*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!BFiVpl-PLlTmBo4LrSj6ULfz94V4okiXi8N_cWD2oi_ajV9ss9GGx4QBsIWriMFC9p03a7scPz5eTI2xr9T1Jx_5W3QweA$
> > > >
> > >
> > >
> > > 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 <
> > > > > >
> > > > >
> > > >
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> *2Fnaviyalall__*3B!!M
> > > >
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> --
> Scott Makeig, Research Scientist and Director, Swartz Center for
> Computational Neuroscience, Institute for Neural Computation, University of
> California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott
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