<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div>Hi Edoardo,</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Edoardo Pinzuti <<a href="mailto:edoardo.pinzuti@gmail.com" class="">edoardo.pinzuti@gmail.com</a>><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">spectral_Granger_causality</b><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">30 May 2019 at 12:16:08 CEST<br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:j.schoffelen@donders.ru.nl" class="">j.schoffelen@donders.ru.nl</a><br class="">
</span></div>
<br class="">
<div class="">
<div dir="ltr" class="">Dear M.J Schoffelen,
<div class=""><br class="">
</div>
<div class="">I am a phd student of the Brain Imaging Center of Frankfurt am Main. I usually take your work on spectral Granger Causality, as reference.</div>
<div class="">I have few short questions on nonparametric GC that I hope you can answer.</div>
<div class=""><br class="">
</div>
<div class="">1) The nonparamteric GC needs the full spectrum decomposition 0 Hz up to Nyquist frequency, is what you usually do ?</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div><br class="">
</div>
<div>Yes.</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">2) I set the Fieldtrip function to granger.conditional='yes' , the output is source-->target conditional on all other sources of the network?</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>I wouldn’t use this functionality, unless you really understand what you are doing. The code is poorly documented, and in general behaves poorly (numerically).</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">
<div dir="ltr" class="">
<div class="">3) I saw that you do the spectral analysis on channels and then project them to source space (multiply with spatial filter) does it make a difference to do the spectral analysis directly on virtual channel data?</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>I don’t know where you saw this, but indeed the order of doing linear transformations of data in general should not make a difference for the result. So: doing a spatial filtering step, followed by an FFT should yield the same result as doing an FFT followed
by a spatial filtering step (provided the same spatial filter is used in both situations).</div>
<div><br class="">
</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">
<div dir="ltr" class="">
<div class="">4) Padding. Would you suggest to pad the data? I have 0.250 ms task length, now I pad the data to 0.400 ms with a spectral resolution of 2.5 Hz and being interested on beta frequencies I use Hanning taper.</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>For the non-parametric spectral factorization to behave well, you need to have sufficiently smooth spectra (as well as a sufficiently high number of frequency bins). I would recommend using somewhat longer time windows (if possible), use zero padding (cfg.pad
in ft_freqanalysis, e.g. of 4), and use the ‘dpss’ + ’tapsmofrq’.</div>
<div><br class="">
</div>
<div>Good luck,</div>
<div>Jan-Mathijs</div>
<div><br class="">
</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">thanks a lot for your help</div>
<div class="">Best,</div>
<div class="">Edoardo</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
</div>
</blockquote>
</div>
<br class="">
</body>
</html>