<div dir="ltr">Dear Constantino,<div><br></div><div>First, you need to specify cfg.dim as the size of the data matrix, in your case probably just [102 500], the size(statobs) before reshaping. Note that you need to put in statobs as a vector (statobs(:)) and statrnd as a numel(statobs) X nRand matrix.</div>
<div><br></div><div>Second, I don't know why you are specifying a cfg.layout, this is not used by the function. The same goes for cfg.neighbours, this is also not used. The higher-level statistics functions convert the cfg.neighbours struct-array into a logical connectivity array using the low-level private function channelconnectivity. To use clusterstat (a low-level function) directly, you need to do this beforehand.</div>
<div><br></div><div>So, do something like this:</div><div><br></div><div>cfg = [];</div><div>cfg.neighbours = neighbours;</div><div>cfg.channel = datachannels; % order is important here, must be the same as the data</div>
<div>connectivity = channelconnectivity(cfg);</div><div><br></div><div>cfg = [];</div><div>...</div><div>cfg.dim = size(statobs); % assuming statobs is still a chan X time matrix</div><div>cfg.connectivity = connectivity;</div>
<div><br></div><div>% this assumes statrnd is a chan X time X nRand array</div><div>statrnd = reshape(statrnd, [numel(statobs), size(statrnd,3)]);</div><div><br></div><div>statobs = statobs(:);</div><div>stat = clusterstat(cfg, statrnd, statobs);</div>
<div><br></div><div>Best,</div><div>Eelke</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 29 August 2014 18:36, Constantino Méndez Bértolo <span dir="ltr"><<a href="mailto:constantino.mendezbertolo@ctb.upm.es" target="_blank">constantino.mendezbertolo@ctb.upm.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear Fieldtrippers</div><div><br></div><div>We have a 3x3 design and MEG data, say only mag channels (n102) to simplify.</div>
<div><br></div><div>We want to perform a cluster-based permutation approach but timelockstatistics (cfg.method = 'montecarlo', cfg.correctm = 'cluster', etc) cannot deal with interactions when you have more than three levels (true?)</div>
<div><br></div><div>So we built our 'statobs' and 'statrnd' doing a GLM in -R Statistical Package- and feed 'clusterstat.m' with them</div><div><br></div><div>We have done this with one channel over time with success. However, I am clueless now about how to solve the problem when dealing with the whole channel set.</div>
<div><br></div><div>I wonder what is the nature of the cfg.dim that we need to feed 'clusterstat.m' with.</div><div><br></div><div>Up to now, we use, (cioming out of -R-):</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">
<div>size(statobs) = nchan*ntime % (102*500) % twin = [0 .5] % seconds</div><div>size(statrnd) = nchan*ntime*nrandomizations % (102*500*1000)</div></blockquote><div><br></div><div>and the following presets:</div><div><br>
</div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>cfg=[];</div><div>cfg.clustercritval = Fcritmain; % We genereate this before hand</div><div>cfg.tail = 1; cfg.clustertail = 1; cfg.clusterthreshold = 'parametric';</div>
<div>cfg.dim = [1 size(statobs,1) size(statobs,2) ] % <<< The key may be here</div><div>load('neuromag306mag_neighb.mat');</div><div>cfg.neighbours = neighbours; </div><div>cfg.feedback = 'yes';</div>
<div>cfg.numrandomization = 1000;</div><div>cfg.clusterstatistic = 'maxsum';</div><div>cfg.layout = 'neuromag306mag.lay';</div><div><span style="white-space:pre-wrap"> </span>for i = 1:length(cfg.neighbours)</div>
<div><span style="white-space:pre-wrap"> </span>cfg.channel{i} = cfg.neighbours(i).label;</div><div><span style="white-space:pre-wrap"> </span>end</div><div><br></div><div>stat = clusterstat(cfg,statrnd, statobs)</div>
</blockquote><div><br></div><div>Which lead us to an error within findcluster </div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Error using findcluster (line 59)</div><div>invalid dimension of spatdimneighbstructmat</div>
<div><br></div><div>Error in clusterstat (line 197)</div><div> posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan);</div></blockquote><div><br></div><div>If anybody has got some insigth it would be greatly appreciated. Or any hints. Are the size of my statobs and starnd correct? I can share more information and firstly apologize if I was not able to describe the problem accurately, I am confused regarding that 'reshape' and the addition of one dimension at "...reshape(postailobs,[cfg.dim,1])...", but the problem arises first when findcluster.m tries to calculate the size of spatdimneighbstructmat</div>
<div><br></div><div>First line of findcluster.m calcualtes 'spatdimlength' by : " spatdimlength = size(onoff, 1);" which in our case is "1", which is obviously wrong?.</div><div><br></div><div>
manythanks&peace2all</div><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br><div><font>Constantino Méndez-Bértolo<br></font></div><div><font>Laboratorio de Neurociencia Clínica,</font><font><span style="font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline"> Centro de Tecnología Biomédica (CTB)</span></font></div>
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