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<p class="MsoNormal">Hi Mr Jan-Mathijs, </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Yes you are right , I get 1s all over the place in the case when I use 0 – 0.5 s.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Okay , thank you very much. Apparently , I need to study more about the tapering method used in frequency analysis.
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I do have 80 trials and I also have 1 more which is the average .
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<p class="MsoNormal">One more question ,please.</p>
<p class="MsoNormal">So my coherence estimates for that just 1 trial (which is the average) and just only 6 tapers used, will still be wrong ??</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you very much</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Kind regards, </p>
<p class="MsoNormal">Chris</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows 10</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:jan.schoffelen@donders.ru.nl">Schoffelen, J.M. (Jan Mathijs)</a><br>
<b>Sent: </b>Thursday, April 29, 2021 10:43 AM<br>
<b>To: </b><a href="mailto:fieldtrip@science.ru.nl">FieldTrip discussion list</a><br>
<b>Subject: </b>Re: [FieldTrip] Question about frequency analysis</p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Chris, <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 notice that you only have a single trial in your data. In Fieldtrip, the unit-of-observation that goes into the coherence computation is the so-called ‘rpttap’ dimension, which is the number of trials times the number of tapers applied.
If this number is 1, then the coherence will be 1, by mathematical definition. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">When the trial length is 0.7 seconds, the specification of tapsmofrq leads to 6 Slepian tapers to be applied (i.e. 2*0.7*5-1), thus to a rpttap of 6 times the number of trials. This brings down the coherence values (but will no doubt still
lead to quite biased estimates, because your input just contains a single trial). With only a 0.2 s window selected, the number of tapers will be 1: (2*0.2*5-1), and thus coherence will indeed trivially go to 1 all over the place. I don’t know what happens
in the 0.5 s case, though, provided your reported all-ones in this case are indeed observed in this situation as well.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Long story short, you should increase the number of trials in your computation, or ramp up the smoothing parameter (the latter makes you lose spectral resolution, so probably that’s undesired).<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"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
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<o:p></o:p></p>
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<p class="MsoNormal">On 29 Apr 2021, at 09:24, Christodoylos Karittevlis <<a href="mailto:christodoylos_k@hotmail.com">christodoylos_k@hotmail.com</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">Dear 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 using the function ft_freqanalysis to calculate power spectrum and cross spectrum and after that I calculate the Magnitude Squared Coherence.<o:p></o:p></p>
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<p class="MsoNormal">The trials are defined to start from -0.200s up to +0.500s .<o:p></o:p></p>
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<p class="MsoNormal">When I use the function ft_freqanalysis on the whole trial it works fine , Coherence gives values from 0 to 1.<o:p></o:p></p>
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<p class="MsoNormal">But when I try to use it only for the prestimulus period (e.g -0.2s – 0s ) or only to the poststimulus period (e.g 0 : 0.5s) , I think it does not work correctly because the Magnitude Squared Coherence is equal to 1 for all the pairs of
channels .<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 if I can calculate the power spectrum and cross spectrum only for prestimulus period or only to the poststimulus period ?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">This is the script that I am using :<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="color:#4472C4">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.output = 'powandcsd';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.method = 'mtmfft';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.foilim = [5 100];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.pad ='nextpow2';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.tapsmofrq = 5;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.keeptrials = 'yes';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.trials = [1] ;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">freq = ft_freqanalysis(cfg, data );</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">data have the structured as the output of ft_preprocessing.<o:p></o:p></p>
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<p class="MsoNormal">When I want to select only the prestimulus or post stimulus period I am using :<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg = [];<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.latency = [-0.2 0] ;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">data_pre = ft_selectdata(cfg,data) ;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">% select only the post stimulus period 0:0.2</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg = [] ;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">cfg.latency = [0 0.5];</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4">data_post = ft_selectdata(cfg,data) ;</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">Thank you in advance!<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Kind regards,<o:p></o:p></p>
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<p class="MsoNormal">Chris<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Sent from<span class="apple-converted-space"> </span><a href="https://urldefense.com/v3/__https:/go.microsoft.com/fwlink/?LinkId=550986__;!!HJOPV4FYYWzcc1jazlU!qTYweIa9rVq5IOMpogVpem_hxn63jpoEOR2mm9J786hT9C72LMok_ZxRD46-sN2WZAUbq-_B$">Mail</a><span class="apple-converted-space"> </span>for
Windows 10<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-size:10.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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