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


---------------------------------------------------------------------------
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.
---------------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20101117/bdcedefc/attachment-0001.html>