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Hi Chris,
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<div class="">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. </div>
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<div class="">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.</div>
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<div class="">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).</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<blockquote type="cite" class="">
<div class="">On 29 Apr 2021, at 09:24, Christodoylos Karittevlis <<a href="mailto:christodoylos_k@hotmail.com" class="">christodoylos_k@hotmail.com</a>> wrote:</div>
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Dear Fieldtrip Community,</div>
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<o:p class=""> </o:p></div>
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I am using the function ft_freqanalysis to calculate power spectrum and cross spectrum and after that I calculate the Magnitude Squared Coherence.</div>
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The trials are defined to start from -0.200s up to +0.500s .</div>
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When I use the function ft_freqanalysis on the whole trial it works fine , Coherence gives values from 0 to 1.</div>
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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 .</div>
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<o:p class=""> </o:p></div>
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Do you know if I can calculate the power spectrum and cross spectrum only for prestimulus period or only to the poststimulus period ?</div>
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<o:p class=""> </o:p></div>
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This is the script that I am using :</div>
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<o:p class=""> </o:p></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg = [];<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.output = 'powandcsd';<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.method = 'mtmfft';<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.foilim = [5 100];<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.pad ='nextpow2';<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.tapsmofrq = 5;<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.keeptrials = 'yes';<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.trials = [1] ;<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">freq = ft_freqanalysis(cfg, data );<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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data have the structured as the output of ft_preprocessing.</div>
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When I want to select only the prestimulus or post stimulus period I am using :</div>
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<span style="color: rgb(68, 114, 196);" class="">cfg = [];<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.latency = [-0.2 0] ;<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">data_pre = ft_selectdata(cfg,data) ;<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class=""><o:p class=""> </o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">% select only the post stimulus period 0:0.2<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg = [] ;<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">cfg.latency = [0 0.5];<o:p class=""></o:p></span></div>
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<span style="color: rgb(68, 114, 196);" class="">data_post = ft_selectdata(cfg,data) ;<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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Thank you in advance!</div>
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<o:p class=""> </o:p></div>
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Kind regards,</div>
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Chris</div>
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<o:p class=""> </o:p></div>
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