[Eeglablist] Advice on filtering strategy before ICA (EEGLAB pipeline; FAA, beta/alpha ratio/ PSD)

Mon May 4 06:52:26 PDT 2026

Hello Makoto,

Thank you so very much for your advice and sharing those resources with me!
I have a follow-up question regarding referencing to the mastoids: in my
script I re-reference to the mastoids, but then remove them from before the
ICA (script pasted below). I do all this before the high-pass filter and
downsampling. I'm using a 64-channel BioSemi, so I could try your
suggestion of using Dezhong Yao's REST, but what might that look like in my
script?
% 3. Re-reference to channels 65 and 66
EEG = pop_reref(EEG, [65 66]);
% 4. Keep only scalp channels 1 through 64
% This removes the reference channels and any other extra sensors
EEG = pop_select(EEG, 'channel', 1:64);
% Save channel locations for later interpolation
original_chanlocs = EEG.chanlocs;
save([filename '_chanlocs.mat'], 'original_chanlocs');
With many thanks, Kathryn

*Kathryn Bolton, MA*

Pronouns: she/her

PhD Candidate | Clinical Psychology

Department of Psychology | Cognitive Aging Lab (CAL)

Toronto Metropolitan University

*E-mail:* *kathryn.bolton at t <kathryn.bolton at ryerson.ca>orontomu.ca
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On Wed, Apr 29, 2026 at 8:01 PM Makoto Miyakoshi via eeglablist <
eeglablist at sccn.ucsd.edu> wrote:

> Hi Kathryn,
>
> But my question about filtering is whether you recommend applying only a
> high-pass
> filter prior to ICA (as above), and then applying the full bandpass (e.g.,
> including a low-pass) later, prior to PSD analysis?
>
>
> Andreas Widmann answered that question once and for all in this 2015 paper.
> 10.1016/j.jneumeth.2014.08.002
>
> The answer is, apply high-pass and low-pass separately, with an
> (inevitably) short transition band width (TBW) to high-pass filter, and a
> gentle TBW for low-pass filter.
> For example, if you want to set a band-pass filter 0.5-55 Hz @-6dB, then
>
> Highpass: cutoff 0.5 Hz (TBW 0.5 * 2 = 1.0)
> Lowpass: cutoff 55 Hz (TBW 5, which makes pass-band edge at 55-5/2 = 52.5
> Hz, and maximum suppression starts at 55+5/2 = 57.5 Hz)
>
> For confirming definitions of terminologies, see this page. This page is a
> summary of my questions and his answers.
>
> https://urldefense.com/v3/__https://eeglab.org/others/Firfilt_FAQ.html__;!!Mih3wA!HPZkz51i3HC_zP7sK-ZAnbc3e7bwYY3dwxbgLZn8v25vAVwmBxhdk6YfF87fgdUWoKXpUNspBYhMnKmFvicAeN5kvEY$
>
> The reason why you want to do this is that you do not want to use an
> unnecessarily steep slope in the low-pass end, which makes the filter order
> unnecessarily long.
>
> Re-reference to linked mastoids prior to ICA (BioSemi recommendations)
>
> My advice: do not use linked mastoids. Physically linked mastoids/earlobes
> is out of the question, this is the worst because electrically your
> subject's head is no longer shaped like a human head (heads are connected
> bilaterally)!!! Digitally linked mastoids/earlobes is also problematic for
> the following reason (from *Electric Fields of the Brain* p. 294, Nunez and
> Srinivasan 2006).
>
> The mathematical linked-ears or linked-mastoids reference may seem to
> provide a "solution" to these problems associated with the physical linked
> reference. However, does the original goal of using the average potential
> of the two ears as the reference make sense? The motivation for this
> procedure is not based on any physical properties of head volume
> conduction. The measured potential difference between a pair of electrodes
> depends on sources located near both electrode positions. With the
> mathematical linked-ears reference, the recorded potential depends on
> sources at three different locations. This approach may further complicate
> the interpretation of scalp potentials and possible source locations rather
> than simplifying it. One rationalization often argued to support the
> linked-ears or linked-mastoids reference is its purported tendency to be a
> "symmetric" reference with respect to both brain hemispheres, thereby
> providing a tool for characterizing hemispheric asymmetries in EEG studies.
> However, this is not generally true; the effect of the average mastoids
> reference is artificially to correlate data from recording electrodes near
> the two mastoids (Srinivasan et al. 1998), potentially reducing estimates
> of dynamic hemispheric source asymmetries. We will consider several
> simulations in the next section where we introduce the average reference
> and compare it to the mathematical linked-ears reference.
>
>
> Instead, use either average reference (if you have > 64 ch) or Dezhong
> Yao's REST (if you use the low number of electrodes, you might want to use
> this, but it is conceptually much more complicated than average reference).
>
> Makoto
>
> On Tue, Apr 28, 2026 at 11:35 PM Kathryn Bolton via eeglablist <
> eeglablist at sccn.ucsd.edu> wrote:
>
> > Hi EEGLAB mailing list,
> >
> > I hope you're having a good week so far! I’m a PhD student working on an
> > EEG study examining affective responses to music in older adults.
> > Participants listen to multiple 1-minute music samples, and I plan to
> > compute frontal alpha asymmetry (FAA) and beta/alpha ratio (PSD-based
> > measures) and relate these to valence/arousal ratings.
> >
> > I’ve structured my pipeline into three stages, partly to distribute work
> > across research assistants:
> >
> >    - *Script 1:* preprocessing + ICA (run by RAs; outputs ICA-ready
> >    datasets)
> >    - *Script 2:* manual ICA inspection/cleaning (topography, spectrum,
> >    timecourse), followed by channel interpolation
> >    - *Script 3:* epoching, PSD computation, and extraction of FAA and
> >    beta/alpha ratio
> >
> > In my original pipeline, I noticed that the component maps used for
> > inspection in Script 2 appeared a bit off (e.g., nearly uniform colour
> > across components). I’ve since revised Script 1 to the following
> workflow:
> >
> >    - Re-reference to linked mastoids prior to ICA (BioSemi
> recommendations)
> >    - High-pass filter at 0.5 Hz only, removing a 50 Hz low-pass filter at
> >    this stage
> >    - Downsample to 512 Hz
> >    - Automated detection and removal of bad channels (logged), prior to
> ICA
> >    - Run ICA using rank-adjusted PCA
> >
> > This seems to have resolved the issue with the component maps. But my
> > question about filtering is whether you recommend applying only a
> high-pass
> > filter prior to ICA (as above), and then applying the full bandpass
> (e.g.,
> > including a low-pass) later, prior to PSD analysis?
> >
> > I want to ensure that the filtering approach is appropriate both for ICA
> > decomposition and for downstream frequency-based analyses (FAA and
> > beta/alpha ratio).
> >
> > Thank you very much for your time and advice, I really appreciate it!
> >
> > Best regards,
> > Kathryn
> >
> >
> > *Kathryn Bolton, MA*
> >
> > Pronouns: she/her
> >
> > PhD Candidate | Clinical Psychology
> >
> > Department of Psychology | Cognitive Aging Lab (CAL)
> >
> > Toronto Metropolitan University
> >
> > *E-mail:* *kathryn.bolton at t <kathryn.bolton at ryerson.ca>orontomu.ca
> > <
> >
> https://urldefense.com/v3/__http://orontomu.ca__;!!Mih3wA!HEf3RTkd7gvWzdftBOsrCvgP_ahawX4XGp6D3OMOOK2ck_zqZyrcOpLjBJdpl7-leggZto82bqKspbCJ49hb7OlEv45uNvcNR5M$
> > >*
> >
> > *Website*: *
> >
> https://urldefense.com/v3/__https://psychlabs.torontomu.ca/cal/portfolio/kathryn-bolton/__;!!Mih3wA!HEf3RTkd7gvWzdftBOsrCvgP_ahawX4XGp6D3OMOOK2ck_zqZyrcOpLjBJdpl7-leggZto82bqKspbCJ49hb7OlEv45uwX-37m8$
> > <
> >
> https://urldefense.com/v3/__https://psychlabs.torontomu.ca/cal/portfolio/kathryn-bolton/__;!!Mih3wA!HEf3RTkd7gvWzdftBOsrCvgP_ahawX4XGp6D3OMOOK2ck_zqZyrcOpLjBJdpl7-leggZto82bqKspbCJ49hb7OlEv45uwX-37m8$
> > >*
> >
> >
> > *Due to the volume of emails I receive, I will do my best to respond
> within
> > 2 business days. If you require an immediate response or if it is an
> > emergency, please put "urgent" in the subject line. Thank you for your
> > understanding. *
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