<div dir="ltr">Hi All,<div><br></div><div>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><div><br></div><div>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><div><br></div><div>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><div><br></div><div>At this point I'm at a loss. Is there something I'm misunderstanding about the algorithm?</div><div><br></div><div>Code below and plot below, channel-by-channel stats attached.</div><div><br></div><div>Thanks!</div><div>Alea<br clear="all"><div><br></div><div>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><div><br></div><div><br></div><div><div>%% THREE CONDITIONS</div><div> %Set up the analysis cfg for 3 conditions (pre- to mid- to post-)</div><div>cfg = []; </div><div>cfg.channel = {'all'};</div><div>cfg.latency = 'all'; </div><div>cfg.frequency = [7 7]; %frequency band indicator</div><div>cfg.avgoverfreq = 'no'; %working on bands not frequencies, so nothing to average</div><div>cfg.method = 'montecarlo'; </div><div>cfg.statistic = 'depsamplesFmultivariate'; %three time points</div><div>cfg.correctm = 'cluster'; </div><div>cfg.clusteralpha = 0.1; %change to .1 because we're computing over averaged bands and time (losing power)</div><div>cfg.clusterstatistic = 'maxsum'; </div><div>cfg.minnbchan = 2; </div><div>cfg.tail = 1; %this has to be 1 for depsamplesF, 0 otherwise</div><div>cfg.clustertail = 1; %this has to be 1 for depsamplesF, 0 otherwise</div><div>cfg.alpha = 0.05; %this has to be 0.05 for depsamplesF, 0.025 otherwise</div><div>cfg.numrandomization = 10000; %to get a min p-value of 0.0001 to account for 500 tests and correction by Bonferroni method.</div><div>%specify which electrodes can form clusters</div><div>cfg_neighb.method = 'distance';</div><div>cfg.neighbours = ft_prepare_neighbours(cfg_neighb, r1t1r_struct);</div><div>%cfg.neighbours = cfgManish.neighbours;</div><div>%cfg = getNeighbours(cfg); % using fixed neighbours</div><div>cfg.layout = layout';</div><div> </div><div><br></div><div>% Set up the design matrixfor 3 conditions</div><div>subj = 27; %will differ based on condition</div><div><br></div><div>design = zeros(2,3*subj);</div><div>for isub = 1:1:subj</div><div> design(1,isub) = isub;</div><div> design(1,subj+isub) = isub;</div><div> design(1,2*subj+isub) = isub;</div><div>end</div><div>design(2,1:subj) = 1;</div><div>design(2,subj+1:2*subj) = 2;</div><div>design(2,2*subj+1:3*subj) = 3;</div><div><br></div><div>cfg.design = design;</div><div>cfg.uvar = 1;</div><div>cfg.ivar = 2;</div><div><br></div><div><br></div><div>% Run the analysis</div><div>[r1r_stat_beta] = ft_freqstatistics(cfg, r1t1r_struct, r1t2r_struct, r1t3r_struct); </div></div><div><br></div><div><br></div><div><div>%Plot the results</div><div>cfg1 = [];</div><div>cfg1.alpha = 0.1;</div><div>cfg1.parameter = 'stat';</div><div>%cfg1.zlim = [0 18.1];</div><div>cfg1.layout = layout';</div><div>cfg1.marker = 'o';</div><div>cfg1.subplotsize = [1 1];</div><div>cfg1.saveaspng = 'r1r_betacluster';</div><div><br></div><div>ft_clusterplot(cfg1, r1r_stat_beta);</div></div><div><br></div><div><br></div><div>***Note non-significant hot spot over left parietal*** </div><div><br></div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span style="font-size:12.8px"><font color="#0b5394"><br></font></span></div><div dir="ltr"><span style="font-size:12.8px"><font color="#0b5394"><br></font></span></div><div dir="ltr"><span style="font-size:12.8px"><font color="#0b5394"><img src="cid:ii_15f31436d6cb6214" alt="Inline image 2" width="427" height="320"><br></font></span></div><div dir="ltr"><span style="font-size:12.8px"><font color="#0b5394"><br></font></span></div><div dir="ltr"><span style="font-size:12.8px"><font color="#0b5394"><br></font></span></div><div dir="ltr"><span style="font-size:12.8px"><font color="#0b5394">Alea C. Skwara</font></span><div><div style="font-size:12.8px"><font color="#0b5394">Graduate Student </font><font color="#f1c232">|</font><font color="#bf9000"> </font><font color="#0b5394">Saron Lab</font></div><div><font color="#f1c232"><a href="http://mindbrain.ucdavis.edu/labs/Saron" target="_blank"><font color="#f1c232">http://mindbrain.ucdavis.edu/labs/Saron</font></a><br></font></div><div style="font-size:12.8px"><font color="#0b5394"><br></font></div><div style="font-size:12.8px"><font color="#0b5394" style="font-size:12.8px">Center for Mind and Brain</font><font color="#f1c232" style="font-size:12.8px"> | </font><span style="font-size:12.8px;color:rgb(11,83,148)">University of California, Davis</span><font color="#0b5394"><br></font></div><div style="font-size:12.8px"><font color="#0b5394">267 Cousteau Place </font><font color="#f1c232">|</font><font color="#0b5394"> Davis CA 95616</font></div><div style="font-size:12.8px"><font color="#0b5394">Cell:</font><font color="#f1c232"> (828) 273-8595</font></div><div style="font-size:12.8px"><blockquote type="cite" style="font-size:12.8px"><div><div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><p></p><font color="#860908"><p></p><p></p><p></p></font><p></p><font color="#860908"></font><p></p></div></blockquote></div></div></blockquote></div><div style="font-size:12.8px"><br></div></div></div></div></div></div></div></div></div></div>
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