[Eeglablist] ICA Misinformation

Stefan Debener stefan.debener at uni-oldenburg.de
Sat Jun 24 03:52:50 PDT 2017


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.pdf
>
> 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%20flow-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.pdf>
> > >
> > >> 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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