[Eeglablist] Statistics for ERSP and ITC

Fri Jul 17 14:59:10 PDT 2020

Dear Laurent,

The baseline correction in epoching is one thing, and the baseline
correction for ERSP/ITC is quite another. The former has no effect on the
latter.
It makes sense that you changed the former and you did not see any
difference in the latter.

To manually specify baseline period for ERSP/ITC for STUDY, you have to use
optional input in STUDY GUI.
Please try it again while using 'baseline', [-1500 -1000] so that mean
value (in dB) between -1500 to -1000 will be used for subtraction.
I predict that this will change the ERSP results.
Meanwhile, ITC result will be the same. There is nothing you can do for the
ITC result.
I care 'ITC randi' and 'ITC spike' have different background noise
distributions... at least I can tell that the color scales are different
between the two plots, if you say the both conditions have the same/similar
number of trials. Maybe you want to show the color bar for the both plots
to make sure of it?

Makoto

On Fri, Jul 10, 2020 at 12:20 AM Laurent Sheybani <Laurent.Sheybani at unige.ch>
wrote:

> Thank you Makoto for your help !
>
> I actually did not apply a baseline correction (given the high signal to
> noise ratio, and the fact that I am just checking if I handle correctly
> Eeglab). For these steps I use EEGLAB's gui. When the window 'Baseline
> removal' pops up after extracting epochs, I just press cancel (as it is
> written to press Cancel if one does not want to remove the baseline).
> However, now that you asked, I tried again, this time extracting epochs
> from -3000 to +1000 ms around markers, and correcting for baseline, using
> as baseline the period of -3000 ms to -2000 ms (the statistics are applied
> after -2000 ms). The results are similar. I also selected an equal number
> of test and control trials, and again obtained the same results (I can
> attached them to this email if you need, but there are really just the
> same...). I feel that I am missing a step in the processing pipeline but I
> can't find where ?
>
> If you have any further idea, I would appreciate again your help !
> Best
> Laurent
>
>
>
> -----Message d'origine-----
> De : eeglablist <eeglablist-bounces at sccn.ucsd.edu> De la part de Makoto
> Miyakoshi
> Envoyé : samedi, 4 juillet 2020 01:30
> À : eeglablist at sccn.ucsd.edu
> Objet : Re: [Eeglablist] Statistics for ERSP and ITC
>
> Dear Laurent,
>
> Wow these are two counterintuitive plots, I agree with you.
> If I were you, I would check the following two things
>
>    1. What's your baseline period in these time-frequency plots? If you use
>    the default, all negative latencies are included, but that would contain
>    half of your spike period.
>    2. How many trials do you have for each condition? Particularly for ITC,
>    SNR of 'background' is directly affected by the number of trials (since
> the
>    resultant vector length is normalized to 0-1, data noisiness/quietness
> in
>    the 'background' is a direct function of number of trials. If two
>    conditions compared have different number of trials, you cannot make
> exact
>    comparison--sometimes all the 'background' (which I means is
> time-frequency
>    window of non-interest) will light up simply because of different noise
>    level. I'm not 100% sure though if this is the case in your example).
>
> I have never used 'use all single trials...' option, so I can't say for
> sure about its effect, but assuming that it is irrelevant here.
>
> Generally speaking, ITC is a cranky measure compared with ERSP. You should
> be careful.
>
> If it does not make sense, please let me know.
>
> Makoto
>
> On Mon, Jun 29, 2020 at 10:28 AM Laurent Sheybani <
> Laurent.Sheybani at unige.ch>
> wrote:
>
> > Dear Eeglabers,
> >
> > I am working on an EEG dataset of a cognitive task and I would like to
> > see whether there is an increase in power and/or ITC around subjects'
> answers.
> > Before analysing these data, I am getting used to the EEGLAB gui using
> > epileptic data that I acquired in the past, just to see whether I
> > process my data correctly in eeglab. I marked all interictal epileptic
> > discharges, so that I know when there is an increase in power.
> >
> > What is very strange is that I find no significant increase in power
> > over the whole window (-2000 to 1000 around interictal epileptic
> > discharges,
> > 3-50 Hz), while the whole window is significant for ITC. I would have
> > expected a significant increase in power around interictal epileptic
> > discharges (as I see it in individual, raw LFP activity) and if there
> > was an increased ITC, I would have expected it to be more specific (in
> > terms of time and frequency range).
> >
> > The pipeline that I follow is:
> >
> >   *   Load data into EEGLAB from a .mat file (1x28822528): 1 electrode,
> > 28822528 timeframes at 16000 Hz sampling frequency.
> >   *   Load the event file
> >   *   Downsampling the data to new sampling frequency = 100 Hz.
> >   *   Export epochs of "spike" and "control" period (-2000 to 1000)
> >   *   Load these .set file into a study (1 subject, 1 session, 2
> > conditions)
> >   *   Study design: Categorical variable: condition - Values (control -
> > spike)
> >   *   Precompute channel measures, selecting ERPs, power spectrum,
> > ERP-image, ERSP and ITC (options for ICA are not chosen, as I have
> > only 1 EEG trace), I keep all default parameters
> >   *   Plot channels measures:
> >      *   Stats:
> >         *   I check "Compute 1st independent variable statistics if any"
> > and "Use single trials for statistics" (I have only 1 subject)
> >         *   Use EEGLAB statistics, permutation statistics, FDR
> correction,
> > statistical threshold 0.05
> >         *   Params: I do not change the parameters.
> >
> > As you can see (power file:
> > https://urldefense.com/v3/__https://www.dropbox.com/s/rwh3b2u8doc8oab/
> > power.jpg?dl=0__;!!Mih3wA!R-vXecxt4S9nEJwpZ1Y3TT5lFDzVkvCPQW8ctGvZlHkO
> > pF7Adw-hqNe9c3QF6ZzjUvrFqg$
> > ) (ITC file:
> > https://urldefense.com/v3/__https://www.dropbox.com/s/npa6f7llnv6tbhl/
> > ITC.jpg?dl=0__;!!Mih3wA!R-vXecxt4S9nEJwpZ1Y3TT5lFDzVkvCPQW8ctGvZlHkOpF
> > 7Adw-hqNe9c3QF6Zwd2CJ8HA$
> > ) there is no increase in power, while there is a non-specific change
> > in ITC.
> >
> > Would any one know where in my processing I did a mistake ? It seems
> > that the ERSP/ITC plots themselves are ok, but the p-values plot are not
> ?
> >
> > Thanks in advance for your help !
> >
> > -----------------------------
> > Dr. Laurent Sheybani, Ph.D
> > Médecin interne en Neurologie Clinique Clinique de Neurologie Hôpitaux
> > Universitaires de Genève Rue Gabrielle-Perret-Gentil, 4
> > 1205 Genève
> > Switzerland
> >
> > _______________________________________________
> > Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> > To unsubscribe, send an empty email to
> > eeglablist-unsubscribe at sccn.ucsd.edu
> > For digest mode, send an email with the subject "set digest mime" to
> > eeglablist-request at sccn.ucsd.edu
> >
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu
> For digest mode, send an email with the subject "set digest mime" to
> eeglablist-request at sccn.ucsd.edu
>