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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Dear Marlies,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>if I am not mistaken, the minnbchan option checks indeed if every channels in a cluster has at least the specified amount of channels in it and removes it otherwise. The code is documented as follows:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> % For every (time,frequency)-element, it is calculated how many significant<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> % neighbours .this channel has If a significant channel has less than minnbchan<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> % significant neighbours, then this channel is removed from onoff.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>If something went wrong is hard to tell – it also depends on how the neighbor structure looks like. If you do not have C3 or C1, then C5 can indeed be defined as a neighbor of Cz, and if you do not have FC2, then Cz could be called a neighbor of FC4. You can check how neighbors are defined by using ft_neighbourplot. That’s the first check I’d do.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Jörn<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><div><p class=MsoNormal><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'>--<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#255A9E;mso-fareast-language:NL'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#255A9E;mso-fareast-language:NL'>Jörn M. Horschig, PhD</span></b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'>, Software Engineer</span><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:black;mso-fareast-language:NL'><o:p></o:p></span></b></p><p class=MsoNormal><a href="http://www.artinis.com/"><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'>Artinis Medical Systems</span></a><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'> | +31 481 350 980 </span><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#255A9E;mso-fareast-language:NL'><o:p></o:p></span></b></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>Marlies Vissers<br><b>Sent:</b> Friday, July 31, 2015 3:27 PM<br><b>To:</b> fieldtrip, donders <fieldtrip@donders.ru.nl><br><b>Subject:</b> [FieldTrip] Effect of cfg.minnbchan<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Dear Fieldtrippers. <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I have a question about the effect of the tuning parameter cfg.minnbchan when performing cluster based permutation testing, since the spatial characteristics of my clusters differ from what I expected to find given the settings I used.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I am running cross-subject correlations (n=31) between a behavioral variable and a subj*channel*time*frequency matrix with power data (preprocessed using EEGlab and decomposed outside of Fieldtrip), using ft_freqstatistics with the function 'ft_statfun_intersubcorr'. Since I'd like to avoid finding clusters with difficult-to-interpret shapes, I set cfg.minnbchan to 2. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>My concern however, is that the resulting clusters do not always exist of neighbouring electrodes. For example, one of the resulting clusters is located at channels C5, Cz & FC4 (EEG, 64 electrodes), which are connected through the other dimensions (time & frequency). In one of Eric Maris' previous replies to an older post about cfg.minnbchan, I read that the parameter cfg.minnbchan only concerns spatial (not time/freq) neighbours. Does this mean that any cluster without spatially neighbouring electrodes should have been rejected when minnbchan is set to 2?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I would be very grateful if someone could let me know whether setting cfg.minnbchan to 2 can -in principle- still yield clusters with spatially-non-adjacent electrodes, or whether this result is likely due to an error in my code. If the latter, I'd very much appreciate advice on checks I could perform to detect the potential error.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The code I used to run this analysis is pasted below.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks in advance!<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Best,<o:p></o:p></p></div><div><p class=MsoNormal>Marlies<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:gray'>Marlies Vissers </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:gray'>PhD student </span><o:p></o:p></p></div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=apple-style-span><span style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:gray'>University of Amsterdam | Department Brain and Cognition | Cognition and Plasticity Laboratory</span></span><span style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=NL style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:gray'>Weesperplein 4 | 1018 XA Amsterdam | 020 - 525 67 24 | </span><a href="mailto:M.E.Vissers@uva.nl"><span lang=NL style='font-size:10.0pt;font-family:"Tahoma",sans-serif'>M.E.Vissers@uva.nl</span></a><span lang=NL style='font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span lang=NL><o:p> </o:p></span></p></div><div><p class=MsoNormal>---<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>% Import the electrode labels from an EEGlab set <o:p></o:p></p></div><div><p class=MsoNormal>elec = ft_read_sens('template_64.set','fileformat','eeglab_set');<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>% Create matrix with TF data<o:p></o:p></p></div><div><p class=MsoNormal>freqData.freq = frex; % Frequenies of TF matrix<o:p></o:p></p></div><div><p class=MsoNormal>freqData.time = tx(TF_idx(1):TF_idx(2))./1000; % Time samples in TF matrix<o:p></o:p></p></div><div><p class=MsoNormal>freqData.dimord = 'subj_chan_freq_time';<o:p></o:p></p></div><div><p class=MsoNormal>freqData.label = elec.label;<o:p></o:p></p></div><div><p class=MsoNormal>freqData.powspctrm = tempTF; % tempTF is matrix with subj*channels*freq*time<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>% Create matrix with behavioral data, make sure the sizes match<o:p></o:p></p></div><div><p class=MsoNormal>behav.freq = frex; <o:p></o:p></p></div><div><p class=MsoNormal>behav.time = tx(TF_idx(1):TF_idx(2))./1000; <o:p></o:p></p></div><div><p class=MsoNormal>behav.dimord = 'subj_chan_freq_time'; % Trick FT: there is just behavioral data in this matrix<o:p></o:p></p></div><div><p class=MsoNormal>behav.label = elec.label;<o:p></o:p></p></div><div><p class=MsoNormal>behav.powspctrm = repmat(accEffect,[1 size(freqData.powspctrm,2),size(freqData.powspctrm,3),size(freqData.powspctrm,4)]); % accEffect is 1*subj array<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>% Set configuration for perm test<o:p></o:p></p></div><div><p class=MsoNormal>% Create cfg and insert parameters<o:p></o:p></p></div><div><p class=MsoNormal>cfg = [];<o:p></o:p></p></div><div><p class=MsoNormal>cfg.latency = [0 1.250];<o:p></o:p></p></div><div><p class=MsoNormal>cfg.frequency = [2 30];<o:p></o:p></p></div><div><p class=MsoNormal>cfg.channel ='all';<o:p></o:p></p></div><div><p class=MsoNormal>cfg.method = 'montecarlo';<o:p></o:p></p></div><div><p class=MsoNormal>cfg.statistic = 'ft_statfun_intersubcorr';<o:p></o:p></p></div><div><p class=MsoNormal>cfg.type = ft_getopt(cfg, 'type', 'Spearman');<o:p></o:p></p></div><div><p class=MsoNormal>cfg.correctm = 'cluster';<o:p></o:p></p></div><div><p class=MsoNormal>cfg.clusteralpha = 0.05; <o:p></o:p></p></div><div><p class=MsoNormal>cfg.clusterstatistic = 'maxsum';<o:p></o:p></p></div><div><p class=MsoNormal>cfg.minnbchan = 2;<o:p></o:p></p></div><div><p class=MsoNormal>cfg.tail = 0;<o:p></o:p></p></div><div><p class=MsoNormal>cfg.clustertail = 0;<o:p></o:p></p></div><div><p class=MsoNormal>cfg.alpha = 0.025;<o:p></o:p></p></div><div><p class=MsoNormal>cfg.numrandomization = 1000; <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>% prepare_neighbours determines what sensors may form clusters: load Biosemi 64 channel cap<o:p></o:p></p></div><div><p class=MsoNormal>cfg.template = [fieldtripdir thisSlash 'template' thisSlash 'neighbours' thisSlash 'biosemi64_neighb.mat'];<o:p></o:p></p></div><div><p class=MsoNormal>cfg.layout = [fieldtripdir thisSlash 'template' thisSlash 'layout' thisSlash 'biosemi64.lay'];<o:p></o:p></p></div><div><p class=MsoNormal>cfg_neighb.method = 'template';<o:p></o:p></p></div><div><p class=MsoNormal>cfg.neighbours = ft_prepare_neighbours(cfg_neighb,freqData);<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>% Create design mat<o:p></o:p></p></div><div><p class=MsoNormal>subj = 31;<o:p></o:p></p></div><div><p class=MsoNormal>design = zeros(2,2*subj);<o:p></o:p></p></div><div><p class=MsoNormal>for i = 1:subj<o:p></o:p></p></div><div><p class=MsoNormal> design(2,i) = i;<o:p></o:p></p></div><div><p class=MsoNormal>end<o:p></o:p></p></div><div><p class=MsoNormal>for i = 1:subj<o:p></o:p></p></div><div><p class=MsoNormal> design(2,subj+i) = i;<o:p></o:p></p></div><div><p class=MsoNormal>end<o:p></o:p></p></div><div><p class=MsoNormal>design(1,1:subj) = 1;<o:p></o:p></p></div><div><p class=MsoNormal>design(1,subj+1:2*subj) = 2;<o:p></o:p></p></div><div><p class=MsoNormal>cfg.design = design;<o:p></o:p></p></div><div><p class=MsoNormal>cfg.ivar = 1; <o:p></o:p></p></div><div><p class=MsoNormal>cfg.uvar = 2; <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>% Run stats<o:p></o:p></p></div><div><p class=MsoNormal>[stat] = ft_freqstatistics(cfg,freqData,behav);<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></body></html>