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Hi Alea,
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<div class="">I think that it all looks OK. I guess that the P5-PO1-O1 cluster is spatially disjoint from the bulk of the suprathreshold data points. Don’t be mislead by the topographical image, where both the contour lines, and the 2D placement of the electrodes
might reflect a picture that is different from what you would expect.</div>
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<div class="">Note, that providing cirange as extra information is not the most informative. Better would have been to show posclusterslabelmat. This data field provides for each sample, whether and to which ‘cluster’ it belongs.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<div class="">On 18 Oct 2017, at 23:05, Alea Skwara <<a href="mailto:acskwara@ucdavis.edu" class="">acskwara@ucdavis.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hi All,
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<div class="">I have been conducting a permutation based cluster analysis using the method = 'montecarlo' correctm= 'cluster' options in ft_freqstatistics to examine longitudinal changes in spectral power. Everything runs just fine and it identifies clusters
successfully.</div>
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<div class="">However, when I examine the results of the analysis, some of the stats strike me as strange. Electrodes that have the highest F values (I am comparing across 3 timepoints) do not test as significant, while electrodes with lower F values do. At
first I thought this was because I had a single "hot" electrode that was not part of a larger cluster, but looking more closely at the stats, it appears that this is not the case.</div>
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<div class="">I have tried double-checking my neighbor definition method and electrode locations to assure that it is not an issue with neighbors being incorrectly registered. I have also tried adjusting the minimum cluster size using the minnbchan option to
ensure it was not an issue of a cluster not reaching the minimum extent. Neither of these options seem to have any impact on the result.</div>
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<div class="">At this point I'm at a loss. Is there something I'm misunderstanding about the algorithm?</div>
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<div class="">Code below and plot below, channel-by-channel stats attached.</div>
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<div class="">Thanks!</div>
<div class="">Alea<br clear="all" class="">
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<div class="">One funky thing to note about this code is that I am inputting average values into the analysis (averaged across time as participants have slightly differing lengths of data, and within bands as I am running this analysis on IAF-based bands, thus
"7" is a dummy code for "mean beta band power", not 7 Hz)</div>
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<div class="">
<div class="">%% THREE CONDITIONS</div>
<div class=""> %Set up the analysis cfg for 3 conditions (pre- to mid- to post-)</div>
<div class="">cfg = []; </div>
<div class="">cfg.channel = {'all'};</div>
<div class="">cfg.latency = 'all'; </div>
<div class="">cfg.frequency = [7 7]; %frequency band indicator</div>
<div class="">cfg.avgoverfreq = 'no'; %working on bands not frequencies, so nothing to average</div>
<div class="">cfg.method = 'montecarlo'; </div>
<div class="">cfg.statistic = 'depsamplesFmultivariate'; %three time points</div>
<div class="">cfg.correctm = 'cluster'; </div>
<div class="">cfg.clusteralpha = 0.1; %change to .1 because we're computing over averaged bands and time (losing power)</div>
<div class="">cfg.clusterstatistic = 'maxsum'; </div>
<div class="">cfg.minnbchan = 2; </div>
<div class="">cfg.tail = 1; %this has to be 1 for depsamplesF, 0 otherwise</div>
<div class="">cfg.clustertail = 1; %this has to be 1 for depsamplesF, 0 otherwise</div>
<div class="">cfg.alpha = 0.05; %this has to be 0.05 for depsamplesF, 0.025 otherwise</div>
<div class="">cfg.numrandomization = 10000; %to get a min p-value of 0.0001 to account for 500 tests and correction by Bonferroni method.</div>
<div class="">%specify which electrodes can form clusters</div>
<div class="">cfg_neighb.method = 'distance';</div>
<div class="">cfg.neighbours = ft_prepare_neighbours(cfg_neighb, r1t1r_struct);</div>
<div class="">%cfg.neighbours = cfgManish.neighbours;</div>
<div class="">%cfg = getNeighbours(cfg); % using fixed neighbours</div>
<div class="">cfg.layout = layout';</div>
<div class=""> </div>
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<div class="">% Set up the design matrixfor 3 conditions</div>
<div class="">subj = 27; %will differ based on condition</div>
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<div class="">design = zeros(2,3*subj);</div>
<div class="">for isub = 1:1:subj</div>
<div class=""> design(1,isub) = isub;</div>
<div class=""> design(1,subj+isub) = isub;</div>
<div class=""> design(1,2*subj+isub) = isub;</div>
<div class="">end</div>
<div class="">design(2,1:subj) = 1;</div>
<div class="">design(2,subj+1:2*subj) = 2;</div>
<div class="">design(2,2*subj+1:3*subj) = 3;</div>
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<div class="">cfg.design = design;</div>
<div class="">cfg.uvar = 1;</div>
<div class="">cfg.ivar = 2;</div>
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<div class="">% Run the analysis</div>
<div class="">[r1r_stat_beta] = ft_freqstatistics(cfg, r1t1r_struct, r1t2r_struct, r1t3r_struct); </div>
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<div class="">
<div class="">%Plot the results</div>
<div class="">cfg1 = [];</div>
<div class="">cfg1.alpha = 0.1;</div>
<div class="">cfg1.parameter = 'stat';</div>
<div class="">%cfg1.zlim = [0 18.1];</div>
<div class="">cfg1.layout = layout';</div>
<div class="">cfg1.marker = 'o';</div>
<div class="">cfg1.subplotsize = [1 1];</div>
<div class="">cfg1.saveaspng = 'r1r_betacluster';</div>
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<div class="">ft_clusterplot(cfg1, r1r_stat_beta);</div>
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<div class="">***Note non-significant hot spot over left parietal*** </div>
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<div dir="ltr" class=""><span style="font-size:12.8px" class=""><font color="#0b5394" class=""><span id="cid:ii_15f31436d6cb6214"><r1r_betacluster_fig1.png></span><br class="">
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<div dir="ltr" class=""><span style="font-size:12.8px" class=""><font color="#0b5394" class="">Alea C. Skwara</font></span>
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<div style="font-size:12.8px" class=""><font color="#0b5394" class="">Graduate Student
</font><font color="#f1c232" class="">|</font><font color="#bf9000" class=""> </font>
<font color="#0b5394" class="">Saron Lab</font></div>
<div class=""><font color="#f1c232" class=""><a href="http://mindbrain.ucdavis.edu/labs/Saron" target="_blank" class=""><font color="#f1c232" class="">http://mindbrain.ucdavis.edu/labs/Saron</font></a><br class="">
</font></div>
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</font></div>
<div style="font-size:12.8px" class=""><font color="#0b5394" style="font-size:12.8px" class="">Center for Mind and Brain</font><font color="#f1c232" style="font-size:12.8px" class=""> | </font><span style="font-size:12.8px;color:rgb(11,83,148)" class="">University
of California, Davis</span><font color="#0b5394" class=""><br class="">
</font></div>
<div style="font-size:12.8px" class=""><font color="#0b5394" class="">267 Cousteau Place
</font><font color="#f1c232" class="">|</font><font color="#0b5394" class=""> Davis CA 95616</font></div>
<div style="font-size:12.8px" class=""><font color="#0b5394" class="">Cell:</font><font color="#f1c232" class=""> (828) 273-8595</font></div>
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