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Dear FIELDTRIP LIST,</div>
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I would like to consult you about how to use ft_clusterplot() to plot clusters at all frequency bands (e.g., theta and alpha) after cluster-based permutation tests.</div>
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A. Goal of Permutation Test</div>
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I hope to compare two conditions and identify clusters for five frequency bands (e.g., theta, delta, alpha, beta, and gamma). The experiment adopted a within subject design where 11 subjects are exposed to trials of both conditions. So I followed the instructions
under the section "Within subject experiments" (<a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq/*within-subjects-experiments__;Iw!!HJOPV4FYYWzcc1jazlU!8Z1b3UdiBLk2aeBDQlpcbEQ6FbwoQ5GqDRyP7Yq5V0N6PLpTRFqRvf3uZV1K8RocmdPlNb-41MiEM2fSvilD-q0X4IE_$" style="margin: 0px; background-color: rgb(255, 255, 255);" class="">https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq/#within-subjects-experiments</a>)
to perform permutation tests on the two conditions. </div>
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B. Results of Permutation Test</div>
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The test reports that there are quite a number of clusters.</div>
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...</div>
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found 36 positive clusters in observed data
<div class="ContentPasted2">found 11 negative clusters in observed data</div>
<div class="ContentPasted2">computing clusters for the thresholded test statistic computed from the randomized design</div>
computing clusters in randomization 500 from 500<br>
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The structure of the statistics results ("stat") looks like this:</div>
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>> stat =
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<div class="ContentPasted3">>>> struct with fields:</div>
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<div class="ContentPasted3">>>>>>>>>> prob: [30×100×101 double]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted4">>>>>>>>>><span class="ContentPasted4"> </span></span>posclusters: [1×36 struct]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted5">>>>>>>>>><span class="ContentPasted5"> </span></span>posclusterslabelmat: [30×100×101 double]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted6">>>>>>>>>><span class="ContentPasted6"> </span></span>posdistribution: [1.9646e+03 762.3575 833.7333 720.9224 655.7105 814.9708
258.9502 533.9392 649.8626 970.1599 497.6544 381.2407 1.2933e+03 992.1687 … ]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted7">>>>>>>>>><span class="ContentPasted7"> </span></span>negclusters: [1×11 struct]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted8">>>>>>>>>><span class="ContentPasted8"> </span></span>negclusterslabelmat: [30×100×101 double]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted9">>>>>>>>>><span class="ContentPasted9"> </span></span>negdistribution: [-1.9270e+03 -439.7888 -394.6326 -257.5007 -3.1617e+03 -1.5213e+03
-981.3342 -821.9707 -1.7823e+03 -1.8166e+03 -471.6444 -614.8437 … ]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted10">>>>>>>>>><span class="ContentPasted10"> </span></span>cirange: [30×100×101 double]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted11">>>>>>>>>><span class="ContentPasted11"> </span></span>mask: [30×100×101 logical]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted12">>>>>>>>>><span class="ContentPasted12"> </span></span>stat: [30×100×101 double]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted13">>>>>>>>>><span class="ContentPasted13"> </span></span>ref: [30×100×101 double]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted14">>>>>>>>>><span class="ContentPasted14"> </span></span>dimord: 'chan_freq_time'</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted15">>>>>>>>>><span class="ContentPasted15"> </span></span>elec: [1×1 struct]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted16">>>>>>>>>><span class="ContentPasted16"> </span></span>freq: [1.1111 1.9444 3.0556 3.8889 5 6.1111 6.9444 8.0556 8.8889 10 11.1111
11.9444 13.0556 13.8889 15 16.1111 16.9444 18.0556 18.8889 … ]</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted17">>>>>>>>>><span class="ContentPasted17"> </span></span>label: {30×1 cell}</div>
<div class="ContentPasted3"><span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted18">>>>>>>>>><span class="ContentPasted18"> </span></span>time: [0 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 0.0800 0.0900
0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 0.1600 0.1700 0.1800 … ]</div>
<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted19">>>>>>>>>><span class="ContentPasted19"> </span></span>cfg: [1×1 struct]<br>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">C. Problem</span><br>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><span class="ContentPasted0 ContentPasted2 ContentPasted23 ContentPasted25" style="font-size:12pt;margin:0px">>>> cfg = []; cfg.alpha = 0.025; </span></span></div>
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>>> cfg.parameter = 'stat'; </div>
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>>> cfg.zlim = [-4 4]; </div>
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>>> cfg.layout = lay; % "lay" stores my layout file.</div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><span class="ContentPasted0 ContentPasted2 ContentPasted23 ContentPasted25" style="font-size:12pt;margin:0px">>>> ft_clusterplot(cfg, stat);</span><br>
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When I try to visualise the clusters using ft_clusterplot() as in the code right above, I encountered the error below:</div>
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>>> Error using ft_clusterplot<br class="ContentPasted26">
>>> if you input time-frequency data this only works if either frequency or time is a singleton dimension<br>
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I read a highly relevant thread (<a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2021-June/040906.html" style="margin: 0px; background-color: rgb(255, 255, 255);" class="ContentPasted29">https://mailman.science.ru.nl/pipermail/fieldtrip/2021-June/040906.html</a>),
and tried to follow the recommendation to plot clusters with <span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted30">ft_multiplotTFR() and <span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted31">ft_topoplotTFR()
as in the code right below, but the plots do not show highlighted clusters.</span></span></div>
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>>> cfg = []; cfg.alpha = 0.025;</div>
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>>> cfg.parameter = 'stat'; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted32">>>><span class="ContentPasted32"> </span></span>cfg.zlim = [-4 4]; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted33">>>><span class="ContentPasted33"> </span></span>cfg.toi = [0 0.6]; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted34">>>><span class="ContentPasted34"> </span></span>cfg.layout = lay; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted35">>>><span class="ContentPasted35"> </span></span>ft_clusterplot(cfg, stat); </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted36">>>><span class="ContentPasted36"> </span></span>cfg.ylim = [3 7]; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted37">>>><span class="ContentPasted37"> </span></span>cfg.maskparameter = 'mask'; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted38">>>><span class="ContentPasted38"> </span></span>cfg.maskstyle = 'outline'; </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted39">>>><span class="ContentPasted39"> </span></span>ft_multiplotTFR(cfg, stat); </div>
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<span style="display: inline !important; background-color: rgb(255, 255, 255);" class="ContentPasted40">>>><span class="ContentPasted40"> </span></span>ft_topoplotTFR(cfg, stat);<br>
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D. Reiteration of Goal of Permutation Test</div>
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I hope to compare the two conditions, and identify clusters for each frequency band (i.e., delta (1-2 Hz), theta (3-7 Hz), alpha (8-13 Hz), beta (13-30 Hz), and gamma (30-100 Hz)) in the time window of interest from 0 ms to 6000 ms.</div>
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Even if the existing functions of Fieldtrip cannot allow plotting cluster-based permutation results of a frequency band, I would like to know how I can identify clusters simply by examining different fields of the permutation test result. </div>
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I will be very appreciative of your help. Thank you so much in advance!!! Also, thank you so much for reading this to this point.</div>
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Best regards,</div>
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Samuel</div>
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