[FieldTrip] Granger causality - parametric and non-parametric calculation

Hähnke, Daniel daniel.haehnke at tum.de
Wed Oct 28 15:41:03 CET 2015

Dear fellow Fieldtrip users,

I am currently computing the Granger causality between LFP signals from different brain regions. As it turns out, this is a more challenging endeavour than I had previously thought. While testing parametric and non-parametric approaches to computing Granger causality, I came across some behaviour which seems odd to me. I hope someone can shed light on these issues:

1. Using the parametric approach (ft_mvaranalysis -> ft_freqanalysis -> ft_connectivityanalysis) I found that ft_freqanalysis can’t deal with MVAR data that contains a trial dimension. The first error is actually that it can’t find the field ‘label’, and this is true: if you run ft_mvaranalysis with cfg.keeptrials = ‘yes’, the resulting structure lacks the ‘label’ field. However, if I manually copy the ‘label’ field from the original data to the MVAR data, ft_freqanalysis stops at some point where it uses an array that lacks one dimension.

2. Using the non-parametric approach (ft_freqanalysis -> ft_connectivityanalysis) I stumbled across the problem that the implementation of Wilson’s algorithm that computes the factorisation of the spectral density matrix doesn’t allow non-integer frequencies nor non-equal distances between frequencies. Is this an inherent limitation of this algorithm?

3. Again for the non-parametric approach: If I use trial-resolved FREQ data for ft_connectivityanalysis, the trial dimension is lost at line 389 if I use data contain a ‘fourierspctrm’ field. If I use data containing a ‘powspctrm’ field, it takes literally hours at line 392 to ‘fix’ the CSD at line 585 in ft_checkdata (which uses ‘fixcsd’) for every trial. This is not resolved by using FREQ data which has both a ‘powspctrm’ as well as a ‘crsspctrm’ field.

I’m not really sure whether I need trial-resolved Granger-causality, but in theory this should be possible. Of course, I could work around this issue by just using 1-trial FREQ data for ft_connectivityanalysis.

Thanks in advance for your ideas!

All the best,

Daniel Hähnke
PhD student

Technische Universität München
Institute of Neuroscience
Translational NeuroCognition Laboratory
Biedersteiner Straße 29, Bau 601
80802 Munich

Email: daniel.haehnke at tum.de
Phone: +49 89 4140 3356

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