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<p class="MsoNormal">Hi Jan-Mathijs,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your response. I have tried your suggestions, but unfortunately the outcome does not change, as the resulting coherence is still unusually high (and that is, for sure, erroneous).</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If the method presented in the tutorial is difficult for a low number of trials, do you know of a better one using FieldTrip ? And, just to be sure I understood the code correctly, what is actually computed as coherence is the magnitude
squared coherence (cross-spectrum over auto-spectrum), right ?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks a lot !</p>
<p class="MsoNormal">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 12 octobre 2021 08:35<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] Unexpectedly high coherence measure</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">I don’t know the algorithmic details of the ‘reference’ approaches’, but:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1) cfg.foi = [1 60] will give you only 2 frequency bins in the output of ft_freqanalysis (with method = ‘mvar’). The mvar method requires a vector of frequency bins.<o:p></o:p></p>
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<p class="MsoNormal">2) 9 segments is really not a lot for a coherence estimate: In the limit of a single segment the coherence goes to 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’d start with changing the cfg.foi into [0:60], (or omitting it altogether) and see what happens.<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">On 11 Oct 2021, at 23:02, 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 FieldTrippers !<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 implementing a script for computing coherence (and Granger causality, but that’s another topic) measure of iEEG data.<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 aware of two different paths in doing so: the parametric and non parametric approaches. As I am still at the early stages of the method, I am using data that was already tested for coherence in another software as reference and performing
the coherence-related steps in FieldTrip, based on the following tutorial :<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://urldefense.com/v3/__https:/www.fieldtriptoolbox.org/tutorial/connectivity/__;!!HJOPV4FYYWzcc1jazlU!qleIR_V3gd0VSeD0kXBxAdiFSlnXmwyrdQCjLUq3kr7Q84KsrWkhIzKdJU_UtL22aaj_LXrrtwTxbCw$">https://www.fieldtriptoolbox.org/tutorial/connectivity/</a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">To summarize, I want to compute the coherence between electrodes X and Y for each frequency from 0 to 60 Hz. The input data consists in 9 segments of 300ms each after preprocessing, fsample 256.0164 Hz.<o:p></o:p></p>
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<p class="MsoNormal">The problem is in the coherence measure I compute. The output of the following script is an unexpectedly high coherence measure, sometimes up to 0.9 when there is supposedly no to little coherence as compared to the « reference » measure
on the other software. However, after searching through the FieldTrip functions code, the way of measuring the coherence seems to be the same (using the cross and auto Spectrum).<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 very most likely missing a step or a parameter in my script, but I have no clue what it is, where it is, and what I am misunderstanding.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Please find here a simplified version of my code for the parametric way of computing coherence.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">% Compute mvar</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg.order = 12; % here I have tried different model orders and the problem persists</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg.toolbox = 'bsmart';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg.channel = {‘X’ ‘Y’};</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">mvar_data = ft_mvaranalysis(cfg, data);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">% Passage fréquence</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg.method = 'mvar';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg.foi = [1 60];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">mvar_freq = ft_freqanalysis(cfg, mvar_data);</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">% Optionnel : cohérence</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">cfg.method = 'coh';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Amasis MT Pro",serif">mvar_coh = ft_connectivityanalysis(cfg, mvar_freq);</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">Do you know what is wrong with this ? I would be very thankful if you could help me on this <span style="font-family:"Segoe UI Emoji",sans-serif">😊</span><o:p></o:p></p>
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<p class="MsoNormal">Thanks a lot !<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"><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!qleIR_V3gd0VSeD0kXBxAdiFSlnXmwyrdQCjLUq3kr7Q84KsrWkhIzKdJU_UtL22aaj_LXrriM-uq7Q$"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!qleIR_V3gd0VSeD0kXBxAdiFSlnXmwyrdQCjLUq3kr7Q84KsrWkhIzKdJU_UtL22aaj_LXrriM-uq7Q$</span></a><o:p></o:p></p>
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