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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Kimaya Sarmukadam <<a href="mailto:ksarmuk2@une.edu.au" class="">ksarmuk2@une.edu.au</a>><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Fw: [FieldTrip] Granger Causality - different range of values based on conditions</b><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">4 February 2019 at 11:07:55 GMT+1<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>" <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
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Hi Jan-Mathijs,
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<div class="">Thank you for your response. After posting, I also realised that frequency range was wrong and extending the frequency range has given me comparable values to the other conditions. </div>
<div class=""><br class="">
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<div class="">For one part of my PhD thesis, I will be comparing functional and effective connectivity measures using the same data set. As I am more interested in comparisons between the methods, in your experience, is it possible to still derive meaningful
data from sensor level connectivity? </div>
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<div class="">Thank you again!</div>
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class=""><br class="">
</div>
<div class="">Kimaya<br class="">
<br class="">
<br class="">
<div style="" class="">
<hr tabindex="-1" style="display: inline-block; width: 728.125px;" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, 4 February 2019 6:13 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Granger Causality - different range of values based on conditions</font>
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<div class="" style="word-wrap: break-word;">Hi Kimaya,
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
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<div class="">
<div class="">
<div class="" style="word-wrap: break-word;">
<div class="" style="word-wrap: break-word;">
<div class="" style="word-wrap: break-word;">J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
<div class="" style="word-wrap: break-word;">Physical location: room 00.028</div>
<div class="" style="word-wrap: break-word;">Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<blockquote type="cite" class="">
<div class="">On 4 Feb 2019, at 02:13, Kimaya Sarmukadam <<a href="mailto:ksarmuk2@une.edu.au" class="OWAAutoLink" id="LPlnk384524" previewremoved="true">ksarmuk2@une.edu.au</a>> wrote:</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Dear Fiedtrippers,</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">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 class="" style="color: rgb(117, 123, 128);"> cfg = [];</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.output = 'fourier';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.method = 'mtmfft';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.channel = {'Fp1', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FT7', 'FC3', 'FCz', 'FC4', 'FT8', 'O1', 'Oz', 'O2', 'T7', 'T8', 'TP7', 'TP8'};</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span><br class="">
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<div class=""><span class="" style="color: rgb(117, 123, 128);">cfg.taper = 'dpss'; </span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.tapsmofrq = 5;</span></div>
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<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.pad = 'maxperlen';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.padtype = 'zero';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.foilim = [13 30];</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><br class="">
<span class="" style="color: rgb(117, 123, 128);"></span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);">cfg = [];</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.method = 'granger';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.granger.method = 'bivariate';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> %cfg.hasjack = '0';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> grangerEC = ft_connectivityanalysis(cfg, freqEC);</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span><br class="">
<span class="" style="color: rgb(117, 123, 128);"></span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg = [];</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.parameter = 'grangerspctrm';</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> cfg.zlim = [0 1];</span></div>
<span class="" style="color: rgb(117, 123, 128);"></span>
<div class=""><span class="" style="color: rgb(117, 123, 128);"> ft_connectivityplot(cfg, grangerEC); </span></div>
<div class=""><br class="">
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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=""><span id="x_cid:5b0676da-26fa-4371-9aef-d945d1139572" class=""><pastedImage.png></span><br class="">
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<div class="">Any help would be greatly appreciated. </div>
<div class=""><br class="">
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<div class="">Kind regards,</div>
<div class=""><br class="">
</div>
<div class="">Kimaya Sarmukadam</div>
<div class=""><br class="">
</div>
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<span class="" 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; float: none; display: inline !important;">_______________________________________________</span><br class="" 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;">
<span class="" 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; float: none; display: inline !important;">fieldtrip
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<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="OWAAutoLink" id="LPlnk874077" previewremoved="true" 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;">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="" 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;">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" class="OWAAutoLink" id="LPlnk11211" previewremoved="true" 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;">https://doi.org/10.1371/journal.pcbi.1002202</a></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="">
<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=""><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></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=""><a href="https://doi.org/10.1371/journal.pcbi.1002202" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></span></div>
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