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Hi Daniel,
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<div class="">As with any connectivity metric that needs a cross-spectrum estimate (and specifically for NPSF-based Granger causality estimates), this estimate needs to make sense. In your case, it doesn’t, for several reasons;</div>
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<div class="">1) you only have a single ’trial’ of data, i.e. for every time point the csd is extremely unstable, and will never-ever give meaningful results numerically, even if the rest of the conditions are favorable.</div>
<div class="">2) in order for the NPSF algorithm to work, the spectral representation needs to be a) smooth, requiring multitapers (+sufficient number of observations) and b) the spectrum needs to be defined from DC to Nyquist.</div>
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<div class="">I recommend you read a bit more in the documentation (and references mentioned) about the underlying algorithmic machinery, and look for some example code in the tutorials/FAQs to get in a more favorable starting position.</div>
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<div class="">Hints:</div>
<div class="">1) forget about the ’time-frequency’ aspect, and focus on frequency only.</div>
<div class="">2) this means that you cut your data into smaller snippets, which are to be used as ovbservations, this can be done with ft_redefinetrial</div>
<div class="">3) then, use ‘mtmfft’ as method for ft_freqanalysis in combination with an appropriate amount of spectral smoothing (’tapsmofrq’) + ‘fourier’ as output.</div>
<div class="">4) then, think about what your data represents (in terms of referencing etc.) -> if you want a full multivariate NPSF while the data are rank deficient (e.g. with a common average, or another funky referencing scheme), the result will probably
be NaN. In which case you’d need to specify cfg.granger.sfmethod = ‘bivariate’, or ditch one of the channels from your multivariate decomposition.</div>
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<div class="">JM</div>
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<blockquote type="cite" class="">
<div class="">On 6 Jul 2019, at 16:23, <a href="mailto:daniel.strahnen@uni-ulm.de" class="">
daniel.strahnen@uni-ulm.de</a> wrote:</div>
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Dear FieldTrip – Community,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span lang="EN-GB" class="">My goal is to analyse changes of Granger Causality over a certain time period.<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class="">Here is the code I use to calculate the wavelet analysis:<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">data.label = {</span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH1'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH2'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH3'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH4'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH5'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH6'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'CH7'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">};</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">data.fsample = 1000;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">% Sampling rate of 1kH</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">data.time{1} = 1:600000;</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">data.trial{1} = Output_data';<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">% Matrix organised as follows:
7 chan x 600000 samples<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">%% Wavelets for time-frequency power analysis</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg = [];</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg.output =<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'powandcsd'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg.method =<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'wavelet'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg.foi = 1:48; <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">% Frequency range from 1 to 48Hz <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">% length
of time window = 0.5 sec</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg.toi = 0:600;<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">% 600 seconds (10min) time period</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">freq_data = ft_freqanalysis(cfg, data);<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="" class="">Up to this point everything seems to be correct, but the granger analysis only gives my NaNs.<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New"; color: forestgreen;" class="">%% Granger causality analysis</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg_conn = [];</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">cfg_conn.method =<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-family: "Courier New"; color: rgb(160, 32, 240);" class="">'granger'</span><span lang="EN-GB" style="font-family: "Courier New";" class="">;</span><span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class="">granger_str = ft_connectivityanalysis(cfg_conn, freq_data);<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-family: "Courier New";" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="" class="">Does anyone has a suggestion what might be the mistake in my code?<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="" class="">Thank you very much and best regards<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" style="" class="">Daniel</span><span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
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