[FieldTrip] Unexpectedly high coherence measure

[Schoffelen, J.M. (Jan Mathijs)]

Hi Eva,

I don’t know the algorithmic details of the ‘reference’ approaches’, but:

1) cfg.foi = [1 60] will give you only 2 frequency bins in the output of ft_freqanalysis (with method = ‘mvar’). The mvar method requires a vector of frequency bins.
2) 9 segments is really not a lot for a coherence estimate: In the limit of a single segment the coherence goes to 1

I’d start with changing the cfg.foi into [0:60], (or omitting it altogether) and see what happens.

Best wishes,
Jan-Mathijs


On 11 Oct 2021, at 23:02, Eva Masson via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hi FieldTrippers !

I am currently implementing a script for computing coherence (and Granger causality, but that’s another topic) measure of iEEG data.

I am aware of two different paths in doing so: the parametric and non parametric approaches. As I am still at the early stages of the method, I am using data that was already tested for coherence in another software as reference and performing the coherence-related steps in FieldTrip, based on the following tutorial :
https://www.fieldtriptoolbox.org/tutorial/connectivity/<https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/connectivity/__;!!HJOPV4FYYWzcc1jazlU!qleIR_V3gd0VSeD0kXBxAdiFSlnXmwyrdQCjLUq3kr7Q84KsrWkhIzKdJU_UtL22aaj_LXrrtwTxbCw$>

To summarize, I want to compute the coherence between electrodes X and Y for each frequency from 0 to 60 Hz. The input data consists in 9 segments of 300ms each after preprocessing, fsample 256.0164 Hz.
The problem is in the coherence measure I compute. The output of the following script is an unexpectedly high coherence measure, sometimes up to 0.9 when there is supposedly no to little coherence as compared to the « reference » measure on the other software. However, after searching through the FieldTrip functions code, the way of measuring the coherence seems to be the same (using the cross and auto Spectrum).

I am very most likely missing a step or a parameter in my script, but I have no clue what it is, where it is, and what I am misunderstanding.

Please find here a simplified version of my code for the parametric way of computing coherence.

% Compute mvar
cfg = [];
cfg.order = 12; % here I have tried different model orders and the problem persists
cfg.toolbox = 'bsmart';
cfg.channel = {‘X’ ‘Y’};
mvar_data = ft_mvaranalysis(cfg, data);

% Passage fréquence
cfg = [];
cfg.method = 'mvar';
cfg.foi = [1 60];
mvar_freq = ft_freqanalysis(cfg, mvar_data);

% Optionnel : cohérence
cfg = [];
cfg.method = 'coh';
mvar_coh = ft_connectivityanalysis(cfg, mvar_freq);

Do you know what is wrong with this ? I would be very thankful if you could help me on this 😊
Thanks a lot !

Cheers !
Eva
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