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Hi Kimaya,
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<div class="">In general I would strongly recommend against estimating and interpreting connectivity using channel level EEG data. There is simply too much linear mixing going on that prohibits a clean enough estimate and honest interpretation.</div>
<div class="">If you wish to insist, however, please note that:</div>
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<div class="">1) Granger causality values in principle do not have an upper bound (i.e. mathematically it is possible that GC>1, although in my experience this hardly ever happens in real data).</div>
<div class="">2) In order to get a mathematically valid estimate of GC using non-parametric spectral factorization, you need to compute the spectrum (in ft_freqanalysis) with the full frequency range, i.e. from 0 Hz to the Nyquist frequency. The frequency range
you have used [13 30] is inadequate.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<div class="">On 4 Feb 2019, at 02:13, Kimaya Sarmukadam <<a href="mailto:ksarmuk2@une.edu.au" class="">ksarmuk2@une.edu.au</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear Fiedtrippers,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have been using the following code to calculate Granger Causality, across various conditions (ranging from 2.5 to 3 minutes long, 4 second epochs). </div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg = [];</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.output = 'fourier';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.method = 'mtmfft';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.channel = {'Fp1', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FT7', 'FC3', 'FCz', 'FC4', 'FT8', 'O1', 'Oz', 'O2', 'T7', 'T8', 'TP7', 'TP8'};</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class="">cfg.taper = 'dpss'; </span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.tapsmofrq = 5;</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.pad = 'maxperlen';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.padtype = 'zero';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.foilim = [13 30];</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class="">cfg = [];</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.method = 'granger';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.granger.method = 'bivariate';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> %cfg.hasjack = '0';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> grangerEC = ft_connectivityanalysis(cfg, freqEC);</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg = [];</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.parameter = 'grangerspctrm';</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> cfg.zlim = [0 1];</span></div>
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<div class=""><span style="color: rgb(117, 123, 128);" class=""> ft_connectivityplot(cfg, grangerEC); </span></div>
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<div class="">For two conditions, the above code was able to evaluate granger causality between 0 and 1. However, for other conditions I am working on currently, the resulting values range from 0 to 4. Therefore, I was wondering whether there is an error in
the code which does not pick up certain data for other conditions.</div>
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<div class="">Below is a visual representation:</div>
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<div class="">Any help would be greatly appreciated. </div>
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<div class="">Kind regards,</div>
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<div class="">Kimaya Sarmukadam</div>
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<span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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