[Eeglablist] ICA Misinformation (Marius Klug)

Marius Klug marius.s.klug at gmail.com
Mon Jul 10 03:15:12 PDT 2017 

Hi everyone,

sorry for the late response!
Thanks a lot for the info, Clayton, this is really helpful and backs up the
discussion to a great degree! It would be nice to have something published
with all the biological artifacts (eye, muscle, heart, skin) that finally
can put the idea of an "artifact-free" EEG at rest... More projects on the
endless to-do list ;-)

Cheers,
Marius

2017-07-07 21:47 GMT+02:00 Joseph Dien <jdien07 at mac.com>:

> I’ve been working on an artifact correction manuscript with an EEG plus
> eye-tracker dataset.  The corneo-retinal dipole (CRD) artifact reflects eye
> position not eye movement so it’ll be constantly present even if the eyes
> maintain fixation.  My take is that each artifact is best corrected with a
> method tailored to its unique characteristics.  I’ve got a working
> algorithm (Multiple Algorithm Artifact Correction or MAAC) implemented in
> my EP Toolkit (https://sourceforge.net/projects/erppcatoolkit/?
> source=navbar) but I need to finish testing and validation.  Ideally it
> also needs to be tested out on different systems and montages to see how
> well it generalizes.
>
> Cheers!
>
> Joe
>
> On Jul 5, 2017, at 07:37, Clayton Hickey <cmhickey at gmail.com> wrote:
>
> Hi Marius, Hi All,
>
> In reading your message, Marius, it struck me that I might make a small
> contribution to this discussion.
>
> The idea that EEG can be free of eye movement artifacts is something that
> can be empirically studied… what is needed is an independent measure of eye
> movements. Many of us have this in concurrent eye-tracking data.
>
> In my group we use an eye-link 1000 and the wonderful EYE-EEG toolbox to
> co-register tracker data with concurrently recorded 64-channel EEG (Dimigen
> et al. & Kliegl, 2011, JEP:GEN). As per the pipeline suggested by Dimigen
> et al., we derive ICA components from the EEG data and identify artifactual
> components as those that strongly correlate with the tracker data. This
> removes some of the ambiguity inherent to identification of artifacts from
> EOG, topography etc, because the IR-camera-based tracker data is
> independent of the encephalic voltage data.
>
> For the fun of it (procrastination, get thee behind me) I just had a quick
> look at a few datasets, extracting intervals where participants maintained
> fixation. I ran infomax ICA on this data and identified ‘artifactual’
> components as those that correlated with the eye-tracking data. I
> consistently got at least a couple of components that strongly correlated
> with the tracker signal. This in spite of the fact that the data was
> putatively ‘artifact-free’ and collected during consistent maintenance of
> fixation.
>
> Some of this variance may come from the brain. Dilation and microsaccades
> are likely to have related neural activity that could be confounded with
> muscle / rotation-of-eyeball activity by ICA. But the brain activity seems
> to be a very small source of variance. The components load heavily on
> frontal sensors close to the eyes, sharply tapering off along the
> anterior-to-posterior axis with very low or zero weights at posterior
> electrodes. I would expect microsaccades and dilation to elicit brain
> activity in subcortex (diffuse topography) or over early visual areas
> (posterior topography).
>
> So... the eyes are doing something to the EEG signal during the
> maintenance of fixation, and ICA can pick this up. This seems to be
> primarily artifact from muscle / eyeball rotation.
>
> best, clayton
>
>
>
>
>
>   8. Re: ICA Misinformation (Marius Klug)
>
> *From: *Marius Klug <marius.s.klug at gmail.com>
> *Subject: **Re: [Eeglablist] ICA Misinformation*
> *Date: *June 30, 2017 at 3:02:52 PM GMT+2
> *To: *otte georges <georges.otte at pandora.be>
> *Cc: *eeglablist <eeglablist at sccn.ucsd.edu>, pnunez at tulane.edu,
> r.srinivasan at uci.edu, Georges Otte <georges.otte at telenet.be>
>
>
> Dear Georges, all,
>
> I am not sure if I missed something, this is the last email about the
> subject to my knowledge, so I'm answering to it now since I feel it should
> get one. My answers are in the text below, I think this will also be my
> first and last email on this topic. Everything I write is my own personal
> opinion.
>
> 2017-06-25 22:18 GMT+02:00 otte georges <georges.otte at pandora.be>:
>
>> 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
>>
>
> I find it strange that you attribute non-scientific way of arguing mostly
> to the ICA experts' side, having followed the complete discussion. I found
> Robert to be rather bold in his statements and kind of immune to
> well-formulated and thought through counter-arguments to his statements,
> even if they are backed up by data and plots. No wonder the tone in the
> discussion has turned a bit darker after a while, if you ask me. We all
> have a lot of things on our plate and must allocate our resources, some of
> the writers have allocated a lot of theirs to the topic and their time and
> reasoning has been met with denial disguised as interest, and statements
> have been repeated even though they were addressed already.
>
>
>> 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
>>
>
> I suspect that not even to be specifically humorous, but an actual
> argument. Robert and other in his side of argument several times spoke of
> "artifact-free data segments" which would be distorted by taking out an ICA
> component, even if it was artifact-free. The argument here is, and I can't
> believe that I have to write this again, since it's been written so often
> already, that no such data exists, end of story. EEG is just an electrical
> recording. Electrical signals are abundant and generated constantly during
> the recording by a wide number of sources, not only the brain. One example
> here being heart beats. Now obviously those signals do have an amplitude
> and a phase, and since they are superpositioning the brain signals and thus
> part of the EEG recording, they will - no way around this! - have an impact
> on the phase (and amplitude) of the data set. The data set is thus
> _continuously_ distorted by the artifact. So by saying that a data set has
> artifact-free time periods, Robert implies that the heart has stopped
> beating, which - as Stefan pointed out - is rather unlikely (now here is a
> bit of humor on my side, I admit ;-) ).
>
> The thing is: This applies not only to heart beats but to each and every
> single artifact source that can be recorded by the EEG! So, even if you
> have no super strong eye blink artifacts, the eyeballs and eye muscles will
> still continuously contaminate the data - a bit at least. Since the IC for
> eyes in a 19 channel data set does likely contain both blinks and
> movements, taking it out will also take out the continuous eye movement
> artifacts produced by all kinds of drifts, saccades, and microsaccades, so
> it will take out parts of the data in the complete set! Now, since the eye
> signal again has a phase and an amplitude, the resulting signal will be
> distorted - but to the better, not to the worse! The new signal does not
> contain the artifacts of the eyes, AT ALL TIME POINTS, at least to the
> degree that ICA was able to separate them. So yes, the phase will be
> distorted, AND THAT IS A GOOD THING! The IC topography should, however, not
> extend to the parietal regions, so there should not be any distortions
> there. You can also check the continuous IC activity (meaning eye activity)
> and at times where it is very low, the distortion in the reconstructed
> sensor channels should be equally low.
>
>
>> 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.
>
>
> The proposed way is to take out the artifact via ICA. That's doable with
> high-density EEG, I find ECG ICs in my subjects without trouble usually. We
> use a neck band with electrodes in addition, that does help a lot, I
> suppose...
>
>
>> 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.
>
>
> This is indeed a non-trivial task and you must be joking to casually
> assume that Stefan will just lay down other projects at hand to have an
> experiment to prove small subleties of heart beat artifact attenuation via
> ICA - that are obvious to the skilled user and will likely not convince
> Robert anyway - in a setup that is likely to contain artifacts from all the
> machines around that are so strong that not much else can be recorded as a
> start. I can see the heart beat in the neck electrodes even visually WHILE
> RECORDING without any preprocessing and ICA, there is no way to deny this.
>
>
>> 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.
>>
>
> Inhowfar does it matter if the eye ball movement artifact is generated in
> to corpus vitreum? I don't see this to be a counter to the notion of a
> dipolar eye ball, it's just a specification. It doesn't matter. The eye
> moves -> signals detectable in the EEG which should be taken out. You're
> giving a straw man argument here.
>
>
>>
>> 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.
>>
>
> Rest assured that the majority of "us scientists" are giving our best to
> investigate our own methods and continuously try to find better ways to
> analyze our data, since we are usually our own most harsh critic and
> overthink everything (at least I am and do)... You however should not have
> stopped with your assessment of cynical humor above but thought further why
> this assumed humorous argument was indeed spot on.
>
> Our serious solution is right there: High-density EEG with spatial
> filtering of some kind (ICA, spatiospectral decomposition, joint
> decorrelation, ...), source localization, source-level analysis or
> back-projection of sources of interest (without artifacts) into the
> sensor-level. Investigating all ICs and seeing the obvious: There are noise
> and artifact signals in the EEG data all the time. Of course it would be
> nice to have and provide you with a really fancy way to have perfect
> brain-only data with 19 electrodes, but at least for the time being, that
> is not possible. Also, I am wondering if you would then still say that it
> is different from the raw data and thus bad, ignoring the arguments
> given... Which brings me to my last point:
>
>
>>
>> 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.
>>
>
> I don't remember anyone attacking Robert as a person, except for the harsh
> tone and bold statements. The "preemptive suppositions" were indeed
> important and correct: He did not provide any information about the ICA
> decomposition and the ICs that were taken out. Since eye movements should
> not extend to the parietal parts of the EEG, but the phase has been altered
> in those channels after back projection, there must have been other ICs
> taken out (possibly containing brain signals) or the decomposition was
> seriously bad (mixing eye and brain signals), which led to doubts of the
> decomposition algorithm, the choice of ICs, and to the general statement
> that 19 channels are rather few for a good ICA decomposition in general. In
> fact, the discussion about his data began when Arno could clearly show that
> taking out eye movement artifacts did NOT distort phase to a relevant
> degree in times other than eye artifacts occurring in one of his earlier
> emails. How Robert can interpret those figures to suit his own argument is
> a mystery to me. Arno was, so to say, not able to replicate your bug and
> then the list proceeded to search for other reasons, but we were stuck by
> the fact, that there was no movement on Roberts side, no careful
> examination of the facts and arguments that have been laid out.
>
> And, again, I can't believe that I have to write this again: YES, TAKING
> OUT ICs WILL ALTER PHASE! This is not even an argument! The thing is a)
> that this is something good for the time points where the artifacts occur,
> because in fact the original data has been distorted by a the artifacts,
> eye in this case, and taking out the artifacts will restore the more
> correct brain signal phases and b) the extent and spatial distribution of
> the distortion presented by Robert led to the conclusion that something
> must have been done incorrectly or at least not with a lot of scrutiny. Who
> knows... workshop participants might make mistakes, they learn, that's what
> they are there for. But this was not addressed by Robert at all.
>
> The arguments and proof have been as sturdy as it can get and the fact
> that you and Robert don't see this just proves that your heads are
> sturdier, sorry to be so clear in my expression. I have nothing personal
> against either you or Robert, I don't know you at all and I don't judge you
> as persons, to be clear, we might get along well over a beer in a bar. I
> just judge the facts and your reactions to them in the emails I read.
>
>
>>
>> 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.
>>
>
> This is the thing. That's what Stefan meant with his "cynical humor
> argument": You cannot seriously argue that physiological signals all of a
> sudden cease to exist every now and then and then come back to life again
> later. Let me be clear:
>
> As long as your subjects have eyes that move, muscles that work, sweat
> glands on their skin, and a beating heart, there are biological artifacts
> in your EEG that continuously contaminate your data by superpositioning
> with the brain signals. And as long as you have electricity in the house
> that you record in, especially if it is close to the electrodes, and no
> faraday cage, you have other noise and artifacts that continuously
> contaminate your signals. This is as true as water is wet and Evolution is
> a thing.
>
> And the best thing is: In times where this is not the case, the continuous
> activation of the IC components would be zero (as long as the decomposition
> is perfect - otherwise at least very low) and there would be no data
> alteration at those times if you subtract that IC! I feel like there should
> be a bit more in-depth understanding ofbiophysics of EEG, ICA, spatial
> filters as a method in general, linear mixture models, etc., before such a
> strong critique against this methods is put forward. Robert may or may not
> have this, but at least to me, from his arguments, it doesn't look like it.
> I don't say this as an attack but rather with the last spark of hope that
> spatial filtering as a useful method gets more understood and not bashed
> into oblivion in the clinics and diagnostics and in the end patients can
> benefit from the advances neuroscience has made in the last 30 years.
>
> Frankly, I am kinda sad about this discussion: It could have been really
> intersting and fruitful, and brought the investigation of ICA as a method
> forward (which would be good, since it's far from perfect and many things
> still need to be tested and learned!) but as someone stated earlier, it's
> mostly interesting from a sociological point of view...
>
> I wish you all the best,
> Marius
>
>
>>
>> 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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