<html><head><base href="x-msg://1415/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Allen,<div><br></div><div>you need bwlabeln anyhow, no matter how you want to cluster (the function can cluster in n-dimensions). so getting the Image Processing Toolbox may be a good investment if you decide to use fieldtrip statistics in future.</div><div><br></div><div>an -untested- alternative may be to use the octave version of bwlabeln. usually the code is very compatible to matlab, i.e. if it does not run out-of-the-box it usually just needs a little tweaking. however it may be a lot slower.</div><div><a href="http://users.powernet.co.uk/kienzle/octave/matcompat/scripts/image/bwlabel.m">http://users.powernet.co.uk/kienzle/octave/matcompat/scripts/image/bwlabel.m</a></div><div><a href="http://www.gnu.org/software/octave/index.html">http://www.gnu.org/software/octave/index.html</a></div><div><br></div><div>good luck,</div><div>nathan</div><div><br></div><div><br><div><div>On 13.05.2010, at 00:44, Allen Ardestani wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi everyone,<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">I am having some difficulty using the cluster-based permutations in both time and frequency domains. I have just 8 channels of discrete LFP positions, so I thought it may be problematic to cluster them together in space. I therefore first tried clustering only in time (ERP) or time-frequency (ERS/ERD) by using a single channel. I used [stat] = ft_timelockstatistics(cfg, ave_spatial, ave_non_spatial) with the following cfg:<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">method: 'montecarlo'<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">statistic: 'indepsamplesT'<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">correctm: 'cluster'<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">clusteralpha: 0.0500<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">clusterstatistic: 'maxsum'<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">tail: 0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">clustertail: 0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">alpha: 0.0250<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">numrandomization: 100<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">design: [1x267 double]<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">channel: 'F1'<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">minnbchan: 0<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">layout: 'layout.mat'<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">ivar: 1<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">I get the following error message:<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">??? Undefined function or method 'bwlabeln' for input arguments of type 'double'.<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Error in ==> findcluster at 89<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "> [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), nfreq, ntime), 4);<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Error in ==> clusterstat at 194<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "> posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan);<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Error in ==> statistics_montecarlo at 321<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource);<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Error in ==> statistics_wrapper at 285<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "> [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource);<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Error in ==> ft_timelockstatistics at 96<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">[stat, cfg] = statistics_wrapper(cfg, varargin{:});<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">I’m assuming that part of the problem is that I don’t have the Image Processing Toolbox, but is there a way to specify to not cluster across channels? I’m a new user, so any advice is much appreciated.<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks in advance!<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10.5pt; font-family: Consolas; ">__________________________________________________________________________________</span><o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Allen Ardestani Email:<span class="Apple-converted-space"> </span><a href="mailto:aardesta@ucla.edu" style="color: blue; text-decoration: underline; ">aardesta@ucla.edu</a><o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Phone: (310) 825-5528<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Medical Scientist Training Program<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">David Geffen School of Medicine at UCLA<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Semel Institute for Neuroscience and Human Behavior<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">760 Westwood Plaza<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Los Angeles, CA 90095-1759<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">USA<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div><p>----------------------------------</p><p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p><p><a href="http://listserv.surfnet.nl/archives/fieldtrip.html" style="color: blue; text-decoration: underline; ">http://listserv.surfnet.nl/archives/fieldtrip.html</a></p><p><a href="http://www.ru.nl/fcdonders/fieldtrip/" style="color: blue; text-decoration: underline; ">http://www.ru.nl/fcdonders/fieldtrip/</a></p></div></blockquote></div><br></div><br><br>
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<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>