[Eeglablist] ICA Misinformation
otte georges
georges.otte at pandora.be
Sun Jun 25 13:18:49 PDT 2017
Dear all
Although I find the subject very interesting, the "cynicism" embedded in some responses feels a bit vexatious and this is something that we should try to avoid in important scientific discussions not unlike this on concerning the possible side effects of ICA signal reconstruction and the model that ICA approach of EEG is based upon
An example: In Prof Debners reply to Dr. Thatcher he invokes the question of the possibility of invisible ECG artefact contamination of the EEG recordings and then continues by saying " because you don't see heart-electrical activity in your "original" 19-ch 10/20 recordings, can you seriously claim that the heart of your participant was not beating during recording?" Ha.. Ha ... ha
The question of possible ECG contamination that Stefan raioses is indeed very important but instead of just joking about it, perhaps it would be even better to (also) propose a possible way to solve this question. I am not in the same scientific league that Prof Debner is in but should that question pop up I would try to search for a test or setup that could clarify it or lead to a solution. Is that not the core of science? I can imagine that at Stefan's university, open hart operations are being performed and it would perhaps be feasible to record EEG before and during the period that the heart function is stopped and a heart-lung machine takes over. I agree that this is not a trivial task due to -among others- the electrical and other potential interferences in the operational theatre and it would require a good research capacity but I am confident that Stefan is up to that task. I think the results would seriously help the community to come closer to a more definite answer. The same could be done for eye movement artefacts. In ophthalmologic clinics all kind of eye diseased are treated. What about people with no corpus vitreum: do they have other eye movement artefacts before and after operation? It is often repeated that eye movement potentials are caused by the cornea-retina dipole. Is that so? Have You people tested this or do You just assumed this is so because it sounds so very plausible. I heard at least one ICA specialist state that this is a mémé and that the corpus vitreous is the originator of those eye movement potentials. I know that all handbooks of EEG claim otherwise so why not test this? We should be very critical with plausible models and try to test the stuff that we all take for granted.
Scientists with access to large university hospital facilities are empowered to solve these kinds of question. They s are the people we clinicians need to get questions solved and personal beliefs or opinions are less relevant in those matters. I can of course understand humor even with a sniff of cynicism but it should not stop there. Humor should not serve to avoid tricky questions as a rapier in a duel but should be followed by an indepth endeavor to prove one point of view in a way that everybody can agree as solid evidence.. I do not want to start a flame war nor do I have revendicate intentions but as a clinician I feel that we deserve a more serious solution from the side of You scientists.
The challenge is open and until now unmet.
When Dr Thatcher launches a potential serious problem, it did not help me very much to hear his data being considered flawed, to hear preemptive suppositions that his choice of ICA algorithm was wrong, that his selection was maybe erroneous etc. One cannot solve a question or a problem by attacking the man who asks the question. It feels like shooting at the pianist because one dislikes the melody. Please bring forward more sturdy arguments and proof that ICA reconstruction does not alter phase.
Considering the EEG as a chaotic multivariate time series continuously contaminated by visible and invisible artefacts is a model that if true justifies the use of ICA but as such a model that needs rock solid scientific confirmation and not just authority based replication of opinions.
Sincerely
Georges Otte
-----Original Message-----
From: eeglablist [mailto:eeglablist-bounces at sccn.ucsd.edu] On Behalf Of Stefan Debener
Sent: Saturday, June 24, 2017 12:53 PM
To: Robert Thatcher <rwthatcher2 at yahoo.com>; Arnaud Delorme <arno at ucsd.edu>
Cc: eeglablist <eeglablist at sccn.ucsd.edu>; pnunez at tulane.edu; r.srinivasan at uci.edu; Georges Otte <georges.otte at telenet.be>
Subject: Re: [Eeglablist] ICA Misinformation
Dear Robert,
Ok, I guess I have to give up on you. Of course you ascribe the "original" times series some magic, and this is one of several flaws in your reasoning. To cite your own published paper:
" PROBLEMS WITH RE-MONTAGING AND DISTORTIONS OF THE ORIGINAL TIME SERIES If the original EEG/event-related potential (ERP) time series is transformed into a second time series by using the average reference then the original phase differences from three electrode locations may be scrambled and lost. For example, with an average reference the entire surface of the brain is not measured, thus the averaging does not create a true zero potential at each instant of time." (citation taken from http://www.appliedneuroscience.com/Coh_phasediff&phase_resetinEEG-ERP.pdf).
Your phrase "distortion of the original time series" does make sense only if you believe that the original time series represents somehow a gold standard, something special (something "magic", forgive my poor use of English) that is magically close to the contributions from brain generators to the surface-recorded signal. In my view this is not justified, for instance because it disregards the fact that recording settings will influence how the data will be recorded, that is, they determine phase and amplitude! I argued before that attributing something special to the "original" time series is highly misleading, the "original" time series is not closer to the brain signal, in contrast it may be pretty far away from it, not only because phase of mixed brain generators does not make much sense, but also becasue of all the artifactual influences not accounted for. Now if you really believe that one particular reference scheme is appropriate in bringing the original data close to the brain while all others are rubbish, then I wish you good luck in trying to convince the community. I predict that nobody will take you serious. The reference discussion has been going on for ages, and there are good reasons to change the reference (online or
offline) depending on what the purpose of the study/analysis is.
I argue that any post-recording signal processing that changes the morphology of a time series will change the phase values as well, NOT just the average reference, and NOT just ICA. In your case, the average reference is far from zero because 19 10-20 channels, which are located on the top half of the head sphere, can hardly sum up to zero. Only a full equidistant spatial coverage of the head sphere would make the spatial average approximate zero potential. Check this paper for in-depth discussion on the average reference and the bias it introduces:
https://www.ncbi.nlm.nih.gov/pubmed/10402104). If you don't like the average reference, fair enough, then simply take any other reference, but you will observe the same "distortion" on phase values. By the way, non-invasive EEG does not measure signals from the brain, there is a skull in between and a couple other layers, all with different conductivies...just another reason to be aware of the inverse problem and trat signals originally recorded from the scalp with great care.
The second flaw in your reasoning is that you believe there are "artifact-free" intervals. The report I included showed (far from perfect, but clearly evident!) heart-electrical activity. Recording parameters strongly determine whether such "EKG" contributions show up in ICA decompositions or not (such as sub-10/20 spatial coverage). Now, only because you don't see heart-electrical activity in your "original"
19-ch 10/20 recordings, can you seriously claim that the heart of your participant was not beating during recording? Of course not! All it says is that the influcene may be stronger or weaker represented in your recordings (depending on individual differences, and, again, recording parameters). With your philosophy, you gonna miss it if it does not jump into your eyes.
Anyway, I hope others join the discussion, I am giving up.
Best,
Stefan
Am 23.06.17 um 19:16 schrieb Robert Thatcher:
>
> Dear Stefan,
>
> Thank you for your dilligence and dedication to this important
> issue. I am pleased that you are in agreement with myself and
> Georges and Gert and scienific publications that "a spatial filter
> operation such as ICA or other, the phase differences may indeed be
> different." I would add that we have not yet found an instance where
> ICA reconstruction did not alter phase differences between channel and
> there I would change the word "may" and phrase to "are indeed different".
>
> You sated: "As a toy example I include the common average reference. "
>
> In Neuroguide we do not allow one to compute phase diffferences or
> coherence when using a common reference. We found with simulation and
> real data that the common reference mixes the phases differences
> between all channels and itself distorts phase differences and often
> in strange ways, for example, if one or two channels has a suddent
> large amplitude alpha or theta rhythm then the phase differences
> between channels that do not have a alpha or beta or theta rhythm are
> altered. If one uses a single common reference then if an alpha
> rhythm appeas for example in O1/2 then there is not change in phase
> differences in channels where there is no alpha. We also compared two
> sine waves at different phase differences, e.g., 30 deg, 60 deg, 90
> deg, etc and mixed different amounts of white noise in one of the
> channels we found linear reductions in coherence (i.e., the phase
> stability over time) as a function of the SNR and the mean phase
> differences were stable until the noise was too high and when
> coherencer was near zero. In contrast, uses the averge refence and
> repeats the same signal and noise test with different phase
> differences then the mean phase difference is quickly lost and there
> is no valid measure of coherence. Here is a url to a publication
> that discusses this topic:
> http://www.appliedneuroscience.com/Coh_phasediff&phase_resetinEEG-ERP.
> pdf
>
> You stated: "Your claim that ICA has somehow corrupted the data such
> that previously super reliable clinical effects all over a sudden
> vanished is not convincing either."
>
> I never said this. There is no ICA reconstruction in NeuroGuide and
> the over 3,000 users of Neuroguide have not complained about coherence
> or phase and they always obtain repeatable measures when the retest
> patients. It was only the WinEEG users that are worried about ICA
> and they never said that they got "super reliable clinical effects".
> They just noticed that coherence using the WinEEG after ICA
> reconstruction was totally different than when they use NxLink or SKIL
> or Neurorep or Neuroguide or Brindx or other software, etc.
>
> You stated: "Now which phase values are valid, those obtained by one
> particular reference scheme or those by another? In my view they are
> both arbitraty"
>
> See my earlier reply regarding average references and the Laplacian
> reference in regard to the accurate and reproducible measures of phase
> differences as opposed to using a single common reference. I am
> recopying the link here:
> http://www.appliedneuroscience.com/Coh_phasediff&phase_resetinEEG-ERP.
> pdf here is another review on this topic:
> http://www.appliedneuroscience.com/Brain%20Connectivity-A%20Tutorial.p
> df
>
> You stated: “there is no such magically clean raw brainsignal
> available in the first place!”
>
> No one says that “magic” is involved in the EEG. However, the physics
> of EEG is involved and during a 5 minute to 20 minute EEG recording
> there is plenty of artifact free data. There are over 100,000 QEEG
> publications in the National Library of Medicine with high effect
> sizes and high test retest reliability and highly reproducible
> findings. My concern and the concern of many others is that ICA
> reconstruction alters phase differences in an entire EEG recording
> even if there are only a few instances of artifact. The reason that
> QEEG has been so successful and so widely used since the late 1950s is
> because people have been successful in avoiding or deleting artifact
> and selecting multiple artifact free parts of the record and achieving
> 0.95 or higher test retest reliability. Over reaction to the
> presence of small amounts of artifact is not a justification for
> altering the electricity of the brain including network dynamics such
> as average synaptic rise times and conduction velocities and couplings
> between groups of neurons.
>
> You stated: “Artifacts not accounted for adulterate EEG phase values”
>
> We agree on this but this is not what the discussion is about. The
> concerns of many is that the phase differences in the artifact free
> sections are altered. Rarely if ever do clinicians/scientists bother
> computing the phase differences during an eye movement artifact.
> Usually phase differences are zero and this physics fact plus the
> electrical gradients from the eyes is how many people detect eye
> movement artifact and then omit the artifact from analyses without
> using ICA. The main focus in QEEG is the parts of the recording
> where there is no artifact and the electrical potentials are generated
> by the brain inside the skull.
>
> Also, thank you for your use of the Hilbert transform, this is only of
> the tools that we use and it allows one to evaluate phase differences
> in every individual time sample in the artifact free sections and
> prove that each and every one of the phase differences for all
> channel combinations is altered by ICA reconstruction. You may be
> interested that we use the Hilbert transform to measure phase shift
> and phase lock duration that have a high correlation with Autism and
> intelligence in short distance connections and with use the Hilbert
> transform to measure the magnitude of information flow (phase slope
> index) and intelligence. Here are some hyperlinks to these studies:
> http://www.appliedneuroscience.com/Intelligence-phase_reset_Nature.pdf
>
> http://www.appliedneuroscience.com/Autism%20Thatcher%20et%20al.pdf
>
> http://www.appliedneuroscience.com/Default_Network_LORETA_Phase_Reset-
> Thatcher_et_al.pdf
>
> http://www.appliedneuroscience.com/Intelligence%20&%20information%20fl
> ow-Thatcher%20et%20al%202016.pdf
>
> We are also using the Hilbert transforms for cross-frequency network
> dynamics including phase-amplitude coupling. I do not believe that
> we would have discovered these important network correlations if we
> had used ICA reconstruction.
>
> Robert
>
>
> On Friday, June 23, 2017, 9:53:01 AM EDT, Stefan Debener
> <stefan.debener at uni-oldenburg.de> wrote:
>
>
> Dear Robert,
>
> I have expanded my illustration and now consider the phase differences
> between two channels, slides 13 to 16 of the updated pdf:
> https://www.dropbox.com/s/e70qhf91dgc5anu/Thatcher_summary_2.pdf?dl=0
>
> Note that phase values were derived by the Hilbert transform of the
> bandpass filtered signal, as explained by W Freeman here:
> http://www.scholarpedia.org/article/Hilbert_transform_for_brain_waves
>
> More details on the particular implementation I used are here:
> https://de.mathworks.com/help/signal/ref/hilbert.html
>
> If you measure phase differences between two channels, consider the
> result as your gold standard, and then apply a spatial filter
> operation such as ICA or other, the phase differences may indeed be
> different. I assume any spatial filter (that effectively spatially
> filters the data) changes phase values and phase difference values. As
> a toy example I include the common average reference. If you apply a
> common average reference to the raw data, then bandpass filter as
> before, and compare the phase difference values to your "gold
> standard", then the phase differences will change as well. Now which
> phase values are valid, those obtained by one particular reference
> scheme or those by another? In my view they are both arbitraty, since
> recording settings as well as preprocessing steps may have a strong
> impact on the actually measured phase. There is no reason to assume
> that a change in phase, or in phase differences, "adulterates" a
> magically clean phase signal obtained from the raw data - simply
> because there is no such magically clean raw brain signal available in the first place!
>
> Your claim that ICA has somehow corrupted the data such that
> previously super reliable clinical effects all over a sudden vanished
> is not convincing either. Artifacts such as eye blinks and lateral eye
> movements are very common, I hope you can agree at least here. Now,
> keep in mind that they contribute fixed spatial patterns - as long as
> the electrodes cap does not shift during acquisition the projections
> of the sources of those artifacts do not change. My illustrations
> above show very clearly how artifacs indeed adulterate phase values,
> just as Arnos illustrations do! Now, if you disregard artifactual
> influences you may end up with highly reliable connectivity effects -
> but they tell you very little about brain function! Even more
> troubling, if you compare two individuals EEGs (say, one "healthy",
> one "abnormal"), then a different amount of artifacts in the data, if
> not carefully taken care of during preprocessing, will produce
> spurious results that are falsely attributed to differences in brain
> function. Actually, given that many artifacts often contribute much
> more variance to that raw signals than (reasonably well validated)
> brain signals, such as fronto-midline theta, this is actually very likely! So, what we learn is that:
>
> Artifacts not accounted for adulterate EEG phase values
>
> Best,
>
> Stefan
>
>
>
> Am 22.06.17 um 20:30 schrieb Robert Thatcher:
> > Dear Stefan,
> > The attachment did not contain any measures of phase differences
> > between channels. It is very difficult to visually see differences
> > in phase differences. One must use the cross-spectrum to calculate
> > phase differences and compare phase differences in degrees. Phase
> > difference varies from -180 to 180 degrees and one must look at the
> > numbers. Below is a url to the two power points that also show
> > visually similar EEG tracings but also computed the instantaneous
> > phase differences using the Hilbert transform (complex demodulation).
> > Four identical time points were selected and they demonstrated
> > totally different phase differences with respect to the O1 channel
> > and the other 18 channels. No matter what reference channel one
> > selects and no matter what identical time points one selects there
> > are always large differences in the phase difference between
> > channels in all frequency bands. I also computed the average phase
> > difference in the artifact free parts of the record and the averages
> > were statistically significantly different at P < 0.0001 and the same for the FFT.
> >
> > Proof of phase difference adulteration is in the power points. I am
> > again copying the hyperlink here:
> >
> >
> >
> http://www.appliedneuroscience.com/Phase_Diff-Original_&_Delorme-Post-
> ICA-4_time_points.zip
> >
> >
> > This cannot be explained by a low quality ICA reconstruction because
> > the ICA reconstruction was conducted by Arnu using EEGLab software.
> >
> > Robert
> > On Thursday, June 22, 2017, 2:00:19 PM EDT, Stefan Debener
> > <stefan.debener at uni-oldenburg.de
> <mailto:stefan.debener at uni-oldenburg.de>> wrote:
> >
> >
> > Dear Robert,
> >
> > I looked up some own data and find absolutely no evidence in favour
> > of your ICA phase adulteration claim, see the attached pdf report. I
> > guess you simply used a poor ICA implementation, and/or a poor
> > component selection. The attached example is in full accordance with
> > Arnos reply, with the difference that I zoom into a clearly visibile
> > alpha oscillation, to have a reference brain signal. The example
> > shows no evidence that occipital alpha phase is biased by ICA eye
> > blink correction. This is a very typical example and based on a
> > quick and dirty ICA decomposition, nothing fancy, to keep this demo
> > simple. Better preprocessing and component selection would easily
> > further improve the signal quality.
> >
> > Best,
> >
> > Stefan
> >
> >
> >
> > Am 20.06.17 um 19:53 schrieb Robert Thatcher:
> > >
> > > Dear Arno,
> > >
> > > 1)*On Phase Differences in the Original vs the Delorme ICA
> > > Reconstruction: *We can agree or disagree about whether or not
> > > some small eye movement artifact was in the hand selection that I
> > > did. But that misses the main point here. That is the ICA
> > > reconstruction alters each and every data point in the entire
> > > record including all artifact free portions no matter what one
> > > selects. For example, the record is 6 minutes and 51 seconds = 411
> > > seconds. The Mitsar sample rate was 250 samples per second =
> > > 102,750 data samples. Phase difference for each frequency band for
> > > each and every one of the
> > > 102,750 data samples has been altered by your own ICA
> > > reconstruction in the EDF file that you emailed to me. Unless you
> > > were to sit next to me or if we do a Team Viewer it is not
> > > possible for me to demonstrate this for all of the data points and
> > > then create a power point for all of these data samples. However,
> > > I can show some exemplars, for example, I have created two figures
> > > at 4 different time points (1 sec;
> > > 2:27 sec; 42 sec & 5:49 sec) that you can download. You can
> > > extract each screen capture and expand them so that you can see
> > > that the exact same time points were selected and the Hilbert
> > > transform JTFA for the
> > > 4 time points resulted in different phase differences in all
> > > channel combinations with respect to O1 for all frequencies. The
> > > same is true no matter which channel is selected to compute the
> > > phase differences in degrees. The same is true also if one
> > > computes averages of the instantaneous phase differences or if one
> > > uses the FFT. Here is the download URL:
> > >
> > >
> >
> http://www.appliedneuroscience.com/Phase_Diff-Original_&_Delorme-Post-
> ICA-4_time_points.zip
> > >
> > >
> > > 2)*On the WinEEG ICA Reconstruction: *I agree that having access
> > > to ICA components themselves and the topography is critical in
> > > understanding exactly what the WinEEG software did. Unfortunately,
> > > I personally do not have access to the WinEEG software.
> > > Clinician/Scientists in Australia use the WinEEG software and they
> > > were the ones that expressed concern about phase difference
> > > distortion at a workshop in Adelaide and gave me the original and
> > > the WinEEG ICA eye movement corrected files in EDF format. They
> > > explained that they removed only one ICA component for eye
> > > movement before they reconstructed a new time series. At first, I
> > > was impressed because the eye movements were absent in the
> > > reconstructed time series. I then was able to use JTFA (Hilbert
> > > transform) to compare the two edf files and discovered that all of
> > > the phase differences for all channels for all frequencies had
> > > been altered by the ICA reconstruction including artifact free
> > > periods. I could demonstrate this by individual time comparisons
> > > or averages of instantaneous phase differences or by the FFT. A
> > > user of WinEEG explained that they do not throw away the original
> > > raw digital data, however I was told that they believe that the
> > > ICA reconstructed times series is artifact free and therefore they
> > > compute means and standard deviations for their normative database
> > > using the ICA reconstructed data and not the hand edited or
> > > artifact deleted original data samples like other commercial
> > > companies do. Your ICA reconstructed time series is actually less
> > > different than the original phase difference in comparison to the
> > > WinEEG ICA. Nonetheless, both your ICA reconstruction and the
> > > WinEEG reconstructions are significantly different than the
> > > original
> recording.
> > >
> > > Best regards,
> > >
> > > Robert
> > >
> > > Cp
> > >
> > >
> > > On Tuesday, June 20, 2017, 1:12:41 AM EDT, Arnaud Delorme
> > > <arno at ucsd.edu <mailto:arno at ucsd.edu> <mailto:arno at ucsd.edu
> <mailto:arno at ucsd.edu>>> wrote:
> > >
> > >
> > > Dear Robert,
> > >
> > > 1) *On my ICA decomposition analysis on your data.* You have
> > > selected a subset of the file where there is 1 minute and 41
> > > second data of eye free data. I was only able to select 40 seconds
> > > in the same file, and I also showed that even in this short file,
> > > there was some residual eye movements. Jason and Stefan agreed
> > > with me. This is the reason why ICA components power spectrum over
> > > frontal channels (and frontal channels only) was affected below 10
> > > Hz frequency band in my data analysis. So on my ICA decomposition,
> > > our disagreement comes from the interpretation. You feel that the
> > > power we remove at low frequency in frontal channel is not eye
> > > movement. In an attempt to convince you, I have picked up a clean
> > > region from your EDF dataset, and did some dipole localization at
> > > this latency. We see that in the clean data, the best dipolar fit
> > > (with 2 symmetrical dipoles) ends up near the eye balls with a
> > > residual variance of 6.9%. Hopefully this convinces you that your
> > > data is not free of eye movement artifacts. If you are willing to
> > > take a step further you might contemplate the idea that ICA can remove this residual spurious activity.
> > >
> > > 2) *On the WinEEG ICA decomposition analysis.* It is critical for
> > > us to see the scalp topography (and if possible continuous
> > > activity) of the components the people at the Australia workshop
> > > selected. Without this, it is not possible for us to comment on
> > > the cleaned data. I agree with you that there was some phase
> > > distortion in alpha (visible directly in the raw data in the first
> > > email you sent) and that this should not be the case. However,
> > > without seing the ICA decomposition, it is not possible for us to
> > > conclude as to wether people selected the wrong ICA components or
> > > if the ICA decomposition implemented in this software is buggy
> > > (ICA is not a simple algorithm and it is sensitive to numerical
> > > imprecision and a lot of other parameters - a suboptimal
> > > implementation could easily explain the WinEEG results). Also, you
> > > seem to imply that the WinEEG people were running ICA on their
> > > data then throwing away the raw data (which is why their ICA
> > > biased neurofeedback database is useless for practical purposes).
> > > Is that correct? One should never throw away the raw data. If they
> > > did throw away the raw data, it is an indication that the WinEEG
> > > are not rigorous in their approach and therefore might not have
> > > implemented ICA in an optimal way. If it is not the case, one may
> > > easily reconstruct the database of measures with or without ICA
> > > decomposition (assuming ICA is done right which does not seem to
> > > be the case) then assess data measure distoritions (power, phase index, etc…) in a statistical fashion.
> > >
> > > Best wishes,
> > >
> > > Arno
> > >
> > > http://sccn.ucsd.edu/~arno/download/clean_edf_file_analysis2.pdf
> <http://sccn.ucsd.edu/%7Earno/download/clean_edf_file_analysis2.pdf%20
> >
> > <http://sccn.ucsd.edu/%7Earno/download/clean_edf_file_analysis2.pdf%
> > 20>
> > > <http://sccn.ucsd.edu/%7Earno/download/clean_edf_file_analysis2.pd
> > > f>
> > >
> > >> On Jun 18, 2017, at 11:44 AM, Robert Thatcher
> > <rwthatcher2 at yahoo.com <mailto:rwthatcher2 at yahoo.com>
> <mailto:rwthatcher2 at yahoo.com <mailto:rwthatcher2 at yahoo.com>>
> > >> <mailto:rwthatcher2 at yahoo.com <mailto:rwthatcher2 at yahoo.com>
> <mailto:rwthatcher2 at yahoo.com <mailto:rwthatcher2 at yahoo.com>>>> wrote:
>
> >
> > >>
> > >> <Pre-ICA-Hand Artifact free selections.edf>
> >
> > >
> > >
> > >
> > > Dieser Nachrichteninhalt wird auf Anfrage komplett heruntergeladen.
> >
> >
>
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