[FieldTrip] granger causality

[jan-mathijs schoffelen]

Hi Tobias,

>
> Q 1:
> If I understood correctly, the grangerspectrum  
> (granger.grangerspctrm) gives me values for the granger-causality in  
> a matrix [nChannel, nChannel, Freqs].
> Does [1,2,:] give me the granger-causality of Channel1 predicting  
> Channel2, or the other way round?
>

The FieldTrip convention is indeed (1,2,:) relates to 1->2

> Q2:
> The plotting function gives me an error:
>
> ft_connectivityplot(cfg, granger)
>
> ??? Error using ==> seloverdim at 36
> cannot select over multiple dimensions at the same time
>
> Error in ==> ft_selectdata at 528
>  if selectchan, data = seloverdim(data, 'chan', selchan, fb); end
>
> Error in ==> ft_connectivityplot at 79
> data        = ft_selectdata(data, 'channel', cfg.channel);

Please update your fieldtrip version. There is a fix (dated 22-04)  
that should take care of this

> Q3:
> How do i statistically validate the measures i get fromthe granger- 
> analysis?
> Is there some recommended statistical test?
> Is it correct to do bootstrapping / permutation testing?
> What I could do on my data is shuffle the trials across conditions,  
> compute granger causality on the shuffeld data, and compair this  
> distribution with the value i get from the data.

This is a very relevant issue. From what you describe it seems as if  
you want to compare across conditions. The shuffling across conditions  
is what we do as well, although it remains open to debate how  
meaningful it is to compare granger causality indices across  
conditions. And, also, if you are able to reject your null-hypothesis,  
whether your decision to reject it is actually due to the actual  
granger causality being different, or by some other confounding  
quantity.

Best wishes,

Jan-Mathijs


> Maybe, somebody is experienced in using granger and could help me out!
> Any advice appreciated!
>
> Thanks a lot!
> tobi
>
>
> I used the following ft_functions according to the online tutorial:
>
> %% MVAR
> cfg         = [];
> cfg.order   = 2;
> cfg.toolbox = 'bsmart';
> mdata       = ft_mvaranalysis(cfg, data);
>
> %% transfer function
> cfg        = [];
> cfg.method = 'mvar';
> mfreq      = ft_freqanalysis(cfg, mdata);
>
> %% granger
> cfg           = [];
> cfg.method    = 'granger';
> granger       = ft_connectivityanalysis(cfg, mfreq);
>
> %%
> cfg        = [];
> cfg.zparam = 'grangerspctrm';
> %cfg.channel = 'all';
> ft_connectivityplot(cfg, granger);
>
> -- 
> Tobias Staudigl
> Fachbereich Psychologie - ZPR
> Postfach ZPR
> 78457 Konstanz
> ZPR, Haus 12
> Tel.: +49 (0)7531 / 88 - 5703
>
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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