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<p class="MsoNormal">Hi Jan-Mathijs,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks a lot ! It works, as I get the kind of structure I wanted.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This also made me realize I did not use ft_mvaranalysis properly, as I don’t get mvar coefficients over time but a repetition of the same coefficients for the n time points. As you said this approach is not ‘good’ for spectrally resolved
Granger causality, I will look into the non parametric approach a little bit more.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks again, and best wishes !</p>
<p class="MsoNormal">Eva</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0cm"><b>De : </b><a href="mailto:fieldtrip@science.ru.nl">Schoffelen, J.M. (Jan Mathijs) via fieldtrip</a><br>
<b>Envoyé le :</b>mardi 22 juin 2021 09:20<br>
<b>À : </b><a href="mailto:fieldtrip@science.ru.nl">FieldTrip discussion list</a><br>
<b>Cc : </b><a href="mailto:janmathijs.schoffelen@donders.ru.nl">Schoffelen, J.M. (Jan Mathijs)</a><br>
<b>Objet :</b>Re: [FieldTrip] Spectrally resolved Granger causality with ft_connectivity_granger</p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Eva, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Apologies, here’s an afterthought: the documentation of the function mentions that the first dimension of the input should be the ‘rpt’ dimension, so I suspect you’d need to shiftdim your input arguments with a ‘-1’.<o:p></o:p></p>
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<p class="MsoNormal">Normally, you’d access ft_connectivity_granger through the higher level function ft_connectivityanalysis, which would take care of this step under-the-hood.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Concretely, probably it works if you do<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">H = shiftdim(freq.transfer,-1);<o:p></o:p></p>
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<p class="MsoNormal">S = shiftdim(freq.crsspctrm,-1);<o:p></o:p></p>
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<p class="MsoNormal">Z = shiftdim(freq.noisecov,-1);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">g = ft_connectivity_granger(H,Z,S,’dimord’,’rpt_chan_chan_freq_time’);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 21 Jun 2021, at 22:28, Eva Masson via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi FieldTrip Community !<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I am trying to compute spectrally resolved Granger causality on (i)EEG data using the parametric approach, with mvar modelling. At this level, it is easier for my data than non parametric modelling.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">From the original data, I have selected two channels to compute Granger causality from channel 1 to channel 2 and from channel 2 to channel 1.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I am currently struggling with the last step, from which I am expecting an output in the form of a 4-D structure containing the Granger causality power for each selected frequency and each time point for :<o:p></o:p></p>
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Channel 1 to channel 1 (not very informative)<o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
Channel 1 to channel 2<o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
Channel 2 to channel 1<o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
Channel 2 to channel 2 (not very informative)<o:p></o:p></li></ul>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">To do so, I am using the function<span class="apple-converted-space"> </span><i>ft_connectivity_granger</i>, which I think is suited for spectrally resolved Granger causality, also while keeping the time dimension.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Here is my sloppy code :<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><i>[mvar_granger, V, n] = ft_connectivity_granger(mvar_freq.transfer, mvar_freq.noisecov, ...</i><o:p></o:p></p>
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<p class="MsoNormal"><i> mvar_freq.crsspctrm, 'dimord', 'chan_chan_freq_time');</i><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">In which mvar_freq is the structure obtained after ft_mvaranalysis and transformed into the frequency domain with ft_freqanalysis_mvar. To be honest, I don’t know what V stands for in the output.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Here are the dimords of the mvar_freq fields used as inputs:<o:p></o:p></p>
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<p class="MsoNormal">Transfer (H) and crsspctrm (S): chan_chan_freq_time<o:p></o:p></p>
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<p class="MsoNormal">Noisecov (Z) : chan_chan_freq<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">After running the previous line, I do not get an error, but a mvar_granger structure in 3D containing a lot of 0 values. Honestly, I don’t really understand what it represents.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">If someone knows how to work with ft_connectivity_granger in such a way that I can get the kind of output I am looking for (probably something like chan_chan_freq_time, right ?), I am all ears to your wisdom !<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I would be very thankful for any help on this topic <span style="font-family:"Segoe UI Emoji",sans-serif">😊</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Cheers !<o:p></o:p></p>
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<p class="MsoNormal">Eva<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">PS : Thanks a lot for this FieldTrip mailing list. I am learning so much thanks to it !<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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</span><a href="https://urldefense.com/v3/__https:/doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!qsFd-6Mz_z_IYoW7fp2Uz2hx-Hk4GXhPN248fH66xtrB8n0cs5bB4qqdcO1zHqqgfhjYa-La7WY4iCo$"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!qsFd-6Mz_z_IYoW7fp2Uz2hx-Hk4GXhPN248fH66xtrB8n0cs5bB4qqdcO1zHqqgfhjYa-La7WY4iCo$</span></a><o:p></o:p></p>
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