Coherence reference channel for statistical analysis

jan-mathijs schoffelen jan.schoffelen at DONDERS.RU.NL
Wed Nov 17 09:56:35 CET 2010 

Dear Rodolphe,

If you have good a priori reasons to only do statistics on a subset of
channel pairs, you may want to constrain ft_connectivityanalysis into
not computing the full NxN coherence matrix. This is possible when you
provide ft_connecitivityanalysis with a field cfg.channelcmb,
specifying the combinations which you would like to compute. Some more
information can be found also in ft_channelcombination. To make it
work smoothly, it is optimal to provide ft_connecitvityanalysis with a
frequency structure containing fourier coefficients
(cfg.output='fourier' prior to calling ft_freqanalysis).

Best

JM


On Nov 10, 2010, at 7:08 PM, Rodolphe Nenert wrote:

> Dear Stanley,
>
> thanks for this very interesting point. Actually i cant go to SFN
> but my boss
> will, and i asked her to go to your talk!
> Anyway, i was in fact looking for a practical way to select a
> reference channel
> with Fieldtrip function ft_freqstatistics.
> The function connectivityanalysis calculated coherence between all
> possible
> channel-pair of electrodes.
> But i dont want to make statistical analysis on all possible pairs,
> so i was
> looking for a cfg parameter in order to select a ref.
> Actually, i copied the the part of the Topographic plot that does
> that, by
> searching the name of the specified ref electrode in all pairs and
> then redraw
> the matrix with only concerned pairs.
>
>
>
>
>
>
> On Tue, 9 Nov 2010 01:17:35 -0800, Stanley Klein <sklein at BERKELEY.EDU>
> wrote:
>
>> Rodolphe, one interesting option for dealing with the EEG problem of
>> reference electrode for coherence is to use Laplacians ("current
>> sources")
>> for each electrode. You may be interested in the pair of papers
>> Winter, et
>> al. J Neuroscience Methods 166 (2007) and Srinivasan, et al.
>> (Statistics in
>> Medicine, 26 2007) that my colleague Jian Ding did with Winter,
>> Srinivasan
>> and Nunez.  They compare Laplacian to regular reference for
>> coherence.
>>
>> I would think that a good approach would be to do it with several
>> types of
>> very different references and compare the differences in coherence.
>>
>> I'm going to be giving a talk on coherence next week at the
>> Neuroscience
>> meeting in San Diego. I'm going to advocate measuring coherence on
>> unfiltered data, but using VERY broad-bandwidth Hilbert pair
>> wavelets, very
>> local in time for doing the coherence. I have several questions on
>> this:
>> 1) Does anyone know whether very broad bandwidth Hilbert pair
>> wavelets
> have
>> been used before? In my mind the locality in time is a useful
>> complement to
>> alternative approaches.
>>
>> 2) Does anyone know whether it has been shown that Morlet and other
>> usual
>> wavelets are not very pretty when only 1 to 1.5 cycles are present.
>> We use
>> what we call Cauchy wavelets.
>>
>> 3) Is there a good reference for the connection of cross-
>> correlation to
>> unnormalized coherence?
>> Let me define what I mean:
>> CC(e1, e2, del) = v(e1, t) v(e2,t-del)           (1)       (using
>> Einstein
>> summation convention
>> Coh(e1, e2, f, n) = V(e1, t,  f, n) V*(e2, t, f, n) , (2) Einstein
>> again
>> implying sum on t.
>> where v is the raw EEG, V is the wavelet transform
>> V(e, t, f, n) = v(e, t+del) * W(del, f, n),      (3)
>> where   W(t, f, n) = 1/(1+ i f t)^n               (4)  for complex,
>> Cauchy
>> Hilbert pair wavelet
>> e1, e2 are the electrodes (unreferenced preferably with referencing
>> to be
>> done at end)
>> t is t, and del is the time shift
>> f is the peak frequency of the wavelet
>> n specifies the bandwidth of the wavelet (sqrt(n) is the number of
>> half
>> cycles)
>>
>> The connection between CC and Coh would be:
>>  Coh(e1, e2, f, n) = CC(e1, e2, t+del) *W(del, f', n')   (5)
>> where  f' and n' are simply connected to f and n but I'm still
>> playing with
>> this to validate it all.
>>
>> I'm very interested in learning whether Eq. 5 connecting unnormalized
>> coherence to cross-correlation is familiar, especially with a
>> pretty closed
>> form time domain expression for the kernel W(del,f',n') in Eq. 5.
>> The SfN
>> meeting is soon, which is why I'm eager to learn whether Eq. 5 is
>> well
>> known. Pretty Hilbert pair filters like W are rare, so I'd be
>> somewhat
>> surprised if Eq. 5 is commonly used. But I'm new to this coherence
>> business
>> so I wouldn't be super surprised.
>>
>> I'd be interested in any feedback. I'll also be happy to meet with
>> anyone
>> interested in coherence at the SfN meeting or at the preceding
>> satellite meeting on "Resting State" before SfN.
>> Stan
>>
>> On Mon, Nov 8, 2010 at 3:48 PM, Rodolphe <batrod at gmail.com> wrote:
>>
>>> Dear Fieldtrip users,
>>>
>>> i take the liberty to ask again my question to you, as i still
>>> didnt find a
>>> solution.
>>> I used ft_connectivityanalysis fuction to get coherence values
>>> between
>>> every channels.
>>> I simply wonder how to select a reference channel to make
>>> statistical
>>> analysis , like when you can select a reference channel to make a
>>> Topographic plot on coherence values.
>>>
>>> Thanks a lot for your help,
>>>
>>> Rodolphe.
>>>
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>>> between users of the FieldTrip toolbox, to share experiences
>>> and to discuss new ideas for MEG and EEG analysis.
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>>> and http://www.ru.nl/neuroimaging/fieldtrip.
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>>>
>>
>> ---------------------------------------------------------------------------
>> You are receiving this message because you are subscribed to
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>> discussion
>> between  users of the FieldTrip  toolbox, to share experiences
>> and to discuss  new ideas for MEG and EEG analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
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>>
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the
> discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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and http://www.ru.nl/neuroimaging/fieldtrip.
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