[FieldTrip] Granger causality with ft_connectivityanalysis

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Tue Sep 1 13:52:40 CEST 2020


Hi Maxime,

Another version of this question has been asked on this discussion list before: https://mailman.science.ru.nl/pipermail/fieldtrip/2019-July/039322.html
I suggest that you read this thread first, and act according to the recommendations.

Please don’t hesitate to ask follow up questions, or if things are not clear, on this current thread.

Best wishes,
Jan-Mathijs



On 1 Sep 2020, at 12:52, Maxime Fauvet <maxime.fauvet at inserm.fr<mailto:maxime.fauvet at inserm.fr>> wrote:


Hello everyone,

I am Maxime Fauvet from ToNIC lab in Toulouse, France, currently working on functional connectivity between brain and muscles during movement through corticomuscular coherence analyses of EEG and EMG signals. I am trying to perform a granger causality (GC) analysis from those signals but somehow I cannot achieve to get a complete time-frequency map of the GC.

I used ft_freqanalysis with the following raw data and cfg:

cfg.method: ‘wavelet’
cfg.output: ‘powandcsq’
cfg.foi: 1:1:50
cfg.pad: 1000

raw data: 2 matrices of 17 trials and 3 seconds sampled at 1KHz, one for EEG and the other for EMG signals, structured as required in ft_freqanalysis

After removing NaNs from powerspectrum and crosspowerspectrum, and setting cfg.method: ‘granger’, I used ft_connectivityanalysis with the cfg and freq (issued from ft_freqanalysis) arguments.

However, I receive the following warning message many times:

Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN.
>In sfactorization_wilson (line 187)
  In ft_connectivity_csd2tranfer (line 267)
  In ft_connectivityanalyis (line 464)

The issue appears to come from the matrix factorization function and more precisely from the chol function, a Matlab core function. Interestingly, some points of the time series do not trigger the warning message.

Can someone tell me if anything is wrong with the use of ft_connectivityanalysis (either in cfg or data)? Any help would be appreciated.

Best wishes,

Maxime



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