Partial Directed Coherence

[jan-mathijs schoffelen]

Dear Ivana,

Yes, it is possible to compute partial coherence. As already
mentioned, I am working on the documentation, but if you are bold
enough to give it a try you may want to look into the code of
ft_connectivityanalysis. What is needed for sure is a field
cfg.partchannel, containing the channel(s) which will be partialized
out. Probably things will work out of the box when the input to
ft_connectivityanalysis as obtained with ft_freqanalysis was generated
with cfg.output = 'fourier'.

Best wishes,

Jan-Mathijs


On Nov 9, 2010, at 1:35 PM, Ivana Konvalinka wrote:

> Thanks Jan-Mathijs, that makes sense.
>
> One more question - is it possible to just do partial coherence in
> fieldtrip?
>
> Best wishes,
>
> Ivana
>
>
>
> On Tue, Nov 9, 2010 at 11:54 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl
> > wrote:
> Dear Ivana,
>
> There is not so much information on the fieldtrip wiki as of yet.
> But I am working on it.
> For the time being, perhaps you know that in order to compute
> partial directed coherence, you need to first fit an autoregressive
> model to your time domain data. This is necessary to obtain a thing
> which is known as the spectral transfer function, from which PDC
> will be derived.
> Therefore you need to do two things before you can call
> ft_connectivityanalysis:
>
> use ft_mvaranalysis to obtain the MVAR-model of your data.
> use ft_freqanalysis (cfg.method = 'mvar') to obtain the spectral
> transfer function.
>
> Note that you do not need to specify partchannel when you will be
> computing pdc; the idea is that by fitting a multivariate model to
> all channels of interest, the 'partialisation' is achieved. At least
> that's the theory...
>
> I hope to find time to work on the documentation soon.
>
> Best wishes,
>
> Jan-Mathijs
>
>
> On Nov 9, 2010, at 11:36 AM, Ivana Konvalinka wrote:
>
>> Hello,
>>
>> I was wondering if it would be possible to get more information on
>> partial directed coherence, using ft_connectivityanalysis. I've
>> been trying to set it up on the frequency data of pairs of EEG
>> electrodes, by partialling out motor evoked fields.
>>
>> Hence, something like this:
>> cfg.method = 'pdc';
>> cfg.channelcmb = { pairs of electrodes here };
>> cfg.partchannel = { electrodes containing fourier spectra of motor
>> events };
>>
>> pdc1 = ft_connectivityanalysis(cfg, freqs);
>>
>> I get the following error: "reference to non-existent field
>> 'transfer'".
>>
>> Is there any more documentation on this method in fieldtrip?
>>
>> Thanks in advance!
>>
>> Ivana
>>
>>
>> --
>> Ivana Konvalinka
>> PhD Student
>> Interacting Minds Group
>> Center of Functionally Integrative Neuroscience
>> University of Aarhus
>> Denmark
>>
>> http://www.interacting-minds.net
>> http://www.cfin.au.dk
>>
>> --------------------------------------------------------------------------- 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
>
> --------------------------------------------------------------------------- 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.
> ---------------------------------------------------------------------------
>
>
>
>
> --
> Ivana Konvalinka
> PhD Student
> Interacting Minds Group
> Center of Functionally Integrative Neuroscience
> University of Aarhus
> Denmark
>
> http://www.interacting-minds.net
> http://www.cfin.au.dk
>
> --------------------------------------------------------------------------- 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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