[FieldTrip] Time-Frequency Plot Granger Causality

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Thu Dec 12 09:28:09 CET 2013

Dear Luckyluke,

In principle what you want should be possible, but it is not well tested. Rather I would suggest to go for solution 2, i.e. re-epoch your data and compile a time-frequency map by hand.
If you want to try it anyway, the key would be to use cfg.method = 'mtmconvol', rather than 'mtmfft' when computing the spectral representation of your data.


On Dec 12, 2013, at 9:19 AM, Lisandro Kaunitz wrote:

> Hi,
> Following the tutorial on connectivity analysis I am trying to implement Granger Causality on simulated signals. I can reproduce all the results that appear in the tutorial in my dataset but I cannot obtain a graph of Wavelet-based granger causality with the format: 
> -x axis: time
> -y axis: frequency
> This  graph should allow me to compare in a single figure how channel 1 granger causes channel 2 at a range of frequencies as a function of time (like in Fig 3 of Dhamala et al, 2008).
> My problem is that I cannot figure out how to produce this graph with the tutorial functions as they seem to automatically compute Granger Spectra for the whole epoch. In the tutorial demo the structure 'freq' has dimord: 'rpttap_chan_freq', and the structure 'granger' has dimord: 'chan_chan_freq'. What I am looking for is a function that returns a structure with the granger spectra computed with dimord of 'chan_chan_freq_time'
> 1- I've tried running 'freq = ft_freqanalysis(cfg, data);' and then '[output] = ft_connectivity_csd2transfer(freq);' with all types of parameters but I could not reach to a solution. Is there a way of building a time-frequency granger spectra within fieldtrip?
> 2- Alternatively to 1, I thought that I could compute non-parametric Granger Spectra for different time windows inside each epoch and then concatenate the results. Before doing this I would like to be sure that I am not missing a way of doing it that it's already implemented in fieldtrip (I have just started using Fieldtrip a short time ago)
> Thanks a lot
> Cheers
> Lisandro Kaunitz
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793


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