[Eeglablist] A tentative issue in coherence calculation in EEGLAB for epoched data

[Iman Mohammad-Rezazadeh]

Hi,
The way the code scripted is to calculate the spectrum from the whole data at once

[alltfX freqs timesout] = timefreq(X, g.srate, spectraloptions{:})

Not each epoch separately and then make an average from them.  and yes in matters !

Best,
Iman
From: Makoto Miyakoshi [mailto:mmiyakoshi at ucsd.edu]
Sent: Thursday, July 23, 2015 3:44 PM
To: Iman Mohammad-Rezazadeh <irezazadeh at UCDAVIS.EDU>
Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>; Loo, Sandra <SLoo at mednet.ucla.edu>; Scott Makeig <smakeig at ucsd.edu>; Chantelle C Kinzel <ckinzel at mednet.ucla.edu>; Michelini, Giorgia <giorgia.michelini at kcl.ac.uk>
Subject: Re: A tentative issue in coherence calculation in EEGLAB for epoched data

Dear Iman,

I ask you this without testing it, but does the order of the averaging process makes difference in results?

Makoto

On Mon, Jul 20, 2015 at 10:09 AM, Iman Mohammad-Rezazadeh <irezazadeh at ucdavis.edu<mailto:irezazadeh at ucdavis.edu>> wrote:

Hi EEGLABERs,
I have been looking into ‘newcrossf’ function and the way it calculates coherence for epoched data. Basically, it uses the ‘timefreq’ function to calculate the time/frequency decomposition the data.  ‘timefreq’ function treats the epoched data as a continuous one:

X = reshape(X, g.frame, g.trials);
[alltfX freqs timesout] = timefreq(X, g.srate, spectraloptions{:});

Y = reshape(Y, g.frame, g.trials);
[alltfY] = timefreq(Y, g.srate, spectraloptions{:});

and calculates the its spectrum using the whole data which is now concatenated version of all trials.  So, for each of channel’s pair (X and Y , for example) the spectrum is calculated as described above and then the joint time-freq decomposition is calculated for coherence value.

coherres = sum(alltfX .* conj(alltfY), 3) ./ sqrt( sum(abs(alltfX).^2,3) .* sum(abs(alltfY).^2,3) );

However, similar to the ERSP concept, each trial/epoch might be different than others [because of perturbations in subjects’ mental status, mental fatigue, etc] and thus I think it is more appropriate to calculate the coherence for each trial first and then make the average across trials.

Any thoughts?
Iman





--
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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