[Eeglablist] ICA Misinformation

Robert Thatcher rwthatcher2 at yahoo.com
Fri Jun 23 10:16:45 PDT 2017

 Dear Stefan,

    Thank you for your dilligence and dedication to thisimportant issue.   I am pleased that you are in agreement with myself andGeorges and Gert and scienific publications that   "aspatial filter operation  such as ICA or other, the phase differencesmay indeed be different."   I would add that we have not yet found aninstance where ICA reconstruction did not alter phase differences betweenchannel and there I would change the word "may" and phrase to"are indeed different".  

You sated:  "As a toy example I include thecommon average reference. "


In Neuroguide we do not allow one to compute phase diffferencesor coherence when using a common reference.  We found with simulation andreal data that the common reference mixes the phases differences between allchannels and itself distorts phase differences and often in strange ways, forexample, if one or two channels has a suddent large amplitude alpha or thetarhythm then the phase differences between channels that do not have a alpha orbeta or theta rhythm are altered.   If one uses a single common referencethen if an alpha rhythm appeas for example in O1/2 then there is not change inphase differences in channels where there is no alpha.  We also comparedtwo 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 foundlinear reductions in coherence (i.e., the phase stability over time) as afunction of the SNR and the mean phase differences were stable until the noisewas too high and when coherencer was near zero.   In contrast, uses theaverge refence and repeats the same signal and noise test with different phasedifferences then the mean phase difference is quickly lost and there is novalid measure of coherence.   Here is a url to a publication thatdiscusses this topic:  http://www.appliedneuroscience.com/Coh_phasediff&phase_resetinEEG-ERP.pdf



You stated:  "Your claim that ICA hassomehow corrupted the data such that previously super reliable clinicaleffects all over a sudden vanished is not convincing either."


I never said this.   There is no ICA reconstruction inNeuroGuide and the over 3,000 users of Neuroguide have not complained aboutcoherence or phase and they always obtain repeatable measures when the retestpatients.   It was only the WinEEG users that are worried about ICA and theynever said that they got "super reliable clinical effects".  They just noticed that coherence using the WinEEG after ICA reconstruction wastotally different than when they use NxLink or SKIL or Neurorep or Neuroguideor Brindx or other software, etc.


You stated:  "Now which phase values are valid, those obtainedby one particular reference scheme or those by another? In my view theyare both arbitraty"


See my earlier reply regarding average references and theLaplacian reference in regard to the accurate and reproducible measures ofphase 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 brain signal available in the firstplace!”


No one says that “magic” is involved in theEEG.  However, the physics of EEG isinvolved and during a 5 minute to 20 minute EEG recording there is plenty ofartifact free data.  There are over100,000 QEEG publications in the National Library of Medicine with high effectsizes and high test retest reliability and highly reproducible findings.   My concern and the concern of many others isthat ICA reconstruction alters phase differences in an entire EEG recordingeven if there are only a few instances of artifact.   The reason that QEEG has been so successfuland so widely used since the late 1950s is because people have been successfulin avoiding or deleting artifact and selecting multiple artifact free parts ofthe record and achieving 0.95 or higher test retest reliability.   Over reaction to the presence of smallamounts of artifact is not a justification for altering the electricity of thebrain including network dynamics such as average synaptic rise times andconduction 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 thediscussion is about.  The concerns ofmany is that the phase differences in the artifact free sections arealtered.   Rarely if ever do clinicians/scientistsbother computing the phase differences during an eye movement artifact.  Usually phase differences are zero and thisphysics fact plus the electrical gradients from the eyes is how many peopledetect eye movement artifact and then omit the artifact from analyses withoutusing ICA.   The main focus in QEEG isthe parts of the recording where there is no artifact and the electricalpotentials are generated by the brain inside the skull.


Also, thank you for your use of the Hilberttransform, this is only of the tools that we use and it allows one to evaluatephase differences in every individual time sample in the artifact free sectionsand prove that each and every one of the phase differences for all  channel combinations is altered by ICAreconstruction.  You may be interestedthat we use the Hilbert transform to measure phase shift and phase lockduration that have a high correlation with Autism and intelligence in shortdistance connections and with use the Hilbert transform to measure themagnitude of information flow (phase slope index) and intelligence.  Here are some hyperlinks to these studies: http://www.appliedneuroscience.com/Intelligence-phase_reset_Nature.pdf





We are also using the Hilbert transforms forcross-frequency network dynamics including phase-amplitude coupling.   I do not believe that we would havediscovered these important network correlations if we had used ICAreconstruction.






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: 

Note that phase values were derived by the Hilbert transform of the 
bandpass filtered signal, as explained by W Freeman here: 

More details on the particular implementation I used are here: 

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



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> 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>> 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>
> >
> >> 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>>> wrote:
> >>
> >> <Pre-ICA-Hand Artifact free selections.edf>
> >
> >
> >
> > Dieser Nachrichteninhalt wird auf Anfrage komplett heruntergeladen.

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