[Eeglablist] Large-volume cross-coherence analysis

[Thomas Ferree]

Will,

I am not sure how EEGLAB is implementing.  For N electrodes, there are
N(N-1)/2 unique pairs.  If EEGLAB is computing coherence for every channel
pair independently, depending upon the implementation, that might involve
computing N(N-1)/2 FFTs for each pair, and that would be slow.  The most
computationally efficient way would be to compute FFTs for each channel once
and for all, then put them into an array, then read that array to compute
the coherence for the pairs.  Perhaps Arno can comment on which of these
approaches is being used in EEGLAB?

Also, a standard trick in any spectral analysis is to make sure that you
have windows with length T equal to power of 2, e.g., 512 points not 500
points in each window, because this makes computation of FFT scale as TlogT,
not T^2.

Finally, a qualitatively different way to approach the problem of many
electrodes is to compute the so-called canonical coherence between sets of
electrodes.  That is a reasonable approach if you are only interested in
coherence between hemispheres, areas, etc.  Here are some references that
might be helpful:

Daniel J. Fletchera, Jonathan Rub, George Feina*  Intra-hemispheric alpha
coherence decreases with increasing cognitive impairment in HIV patients.
 Electroencephalography and clinical Neurophysiology 102 (1997) 286-294 –
Careful there is a mathematical typo in the appendix.

A. A. Lyubushin, Jr.  Analysis of Canonical Coherences in the Problems of
Geophysical Monitoring Izvestiya, Physics of the Solid Earth, Vol. 34, No.
1, 1998, pp. 52–58. Translated from Fizika Zemli, No. 1, 1998, pp. 59–66.


David J. Thomson

GENERALIZED COHERENCES BETWEEN VECTOR DATA ON TWO SPACECRAFT

1-4244-0309-X/06/$20.00 ©2006 IEEE


J. TIMMER et al,

CROSS-SPECTRAL ANALYSIS OF TREMOR TIME SERIES



International Journal of Bifurcation and Chaos, Vol. 10, No. 11 (2000)
2595–2610

I have implemented a canonical coherence function that reads in the EEGLAB
data structure, and am willing to share if you are interested.

Best,
Tom.

-- 
Thomas Ferree, PhD
Cell: (415) 577-1285

On Mon, Feb 21, 2011 at 10:06 AM, Will Sedley <willsedley at gmail.com> wrote:

> Dear EEGlab experts,
>
> I would be grateful for any help on this.
>
> I have a dataset of about 190 channels (which I have cut down from
> around 1400), and am needing to compute cross-coherence between every
> channel and every other channel.
>
> Presently I am running newcrossf for every channel combination, which
> means running it approx 18,000 times per condition. I have limited the
> resolution to 2 time points and 30 frequency to speed things up, but
> it still takes 5-10 hours to run.
>
> I am wondering if there is a way to do this a more
> computationally-efficient way. e.g. is there a way to compute
> coherence just based on the complex part of the last output argument
> of newtimef? Then perhaps I could just run a time/frequency
> decomposition once per channel, and then do some further computations
> to obtain the coherences.
>
> If anyone can suggest how to go about this (or an equivalent method),
> or even provide any code to help with this, then I would be extremely
> grateful.
>
> Many thanks in advance and best wishes,
> Will
> _______________________________________________
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20110223/913c12e7/attachment.html>