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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Hi Allen,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Thank
you very much for the input – I got the Image Processing Toolbox and am now
able to make use of the clustering function. I do have remaining
questions about the cluster analysis. I tried looking at the code but
still can’t figure out what type of clustering approach (e.g., k-means, fuzzy
logic, etc) is being used and how to adjust its clustering sensitivity,
independent of the cluster thresholding alpha. Any help would be much
appreciated!<o:p></o:p></span></p>
</div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>I know it’s a bit pretentious to refer to one’s own papers, but
this is a case where the question forces me:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Maris & Oostenveld (2007). Journal of Neuroscience Methods.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Good luck,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Eric<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>dr. Eric Maris<br>
Donders Institute for Brain, Cognition and Behavior<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Center for Cognition and F.C. Donders Center for Cognitive
Neuroimaging<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Radboud University</span><span lang=EN-US style='font-size:11.0pt;
font-family:"Verdana","sans-serif";color:#1F497D'><br>
</span><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>P.O. Box 9104</span><span lang=EN-US style='font-size:11.0pt;
font-family:"Verdana","sans-serif";color:#1F497D'><br>
</span><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>6500 HE Nijmegen<br>
The Netherlands<br>
T:+31 24 3612651<br>
Mobile: 06 39584581<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>F:+31 24 3616066<br>
E: e.</span><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><a href="mailto:e.maris@donders.ru.nl"
title="blocked::mailto:maris@nici.kun.nl"><span lang=DE>maris@donders.ru.nl</span></a></span><span
lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> FieldTrip discussion list
[mailto:FIELDTRIP@NIC.SURFNET.NL] <b>On Behalf Of </b>Nathan Weisz<br>
<b>Sent:</b> Thursday, May 13, 2010 1:22 AM<br>
<b>To:</b> FIELDTRIP@NIC.SURFNET.NL<br>
<b>Subject:</b> Re: [FIELDTRIP] Error in timelockstatistics<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Dear Allen,<o:p></o:p></span></p>
<div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US>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.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US>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.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US><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><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US><a
href="http://www.gnu.org/software/octave/index.html">http://www.gnu.org/software/octave/index.html</a><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US>good luck,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US>nathan<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<div>
<div>
<p class=MsoNormal><span lang=EN-US>On 13.05.2010, at 00:44, Allen Ardestani
wrote:<o:p></o:p></span></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><span lang=EN-US><o:p> </o:p></span></p>
<div>
<div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi
everyone,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;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></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>method:
'montecarlo'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>statistic:
'indepsamplesT'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>correctm:
'cluster'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>clusteralpha:
0.0500<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>clusterstatistic:
'maxsum'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>tail:
0<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>clustertail:
0<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>alpha:
0.0250<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>numrandomization:
100<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>design:
[1x267 double]<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>channel:
'F1'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>minnbchan:
0<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>layout:
'layout.mat'<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>ivar:
1<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
get the following error message:<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>???
Undefined function or method 'bwlabeln' for input arguments of type 'double'.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Error
in ==> findcluster at 89<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
[labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :),
nfreq, ntime), 4);<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Error
in ==> clusterstat at 194<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
posclusobs = findcluster(reshape(postailobs,
[cfg.dim,1]),channeighbstructmat,cfg.minnbchan);<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Error
in ==> statistics_montecarlo at 321<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
[stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource);<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Error
in ==> statistics_wrapper at 285<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
[stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource);<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Error
in ==> ft_timelockstatistics at 96<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>[stat,
cfg] = statistics_wrapper(cfg, varargin{:});<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;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></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Thanks
in advance!<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:10.5pt;font-family:Consolas'>__________________________________________________________________________________</span><span
lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Allen
Ardestani Email:<span class=apple-converted-space> </span><a
href="mailto:aardesta@ucla.edu">aardesta@ucla.edu</a><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Phone:
(310) 825-5528<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Medical
Scientist Training Program<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>David
Geffen School of Medicine at UCLA<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Semel
Institute for Neuroscience and Human Behavior<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>760
Westwood Plaza<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Los
Angeles, CA 90095-1759<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>USA<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
</div>
<p><span lang=EN-US>----------------------------------<o:p></o:p></span></p>
<p><span lang=EN-US>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.<o:p></o:p></span></p>
<p><span lang=EN-US><a href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a><o:p></o:p></span></p>
<p><span lang=EN-US><a href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a><o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><span lang=EN-US><o:p> </o:p></span></p>
<p><span lang=EN-US>----------------------------------<o:p></o:p></span></p>
<p><span lang=EN-US>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.<o:p></o:p></span></p>
<p><span lang=EN-US>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></span></p>
<p><span lang=EN-US>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></span></p>
<p>----------------------------------<o:p></o: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.<o:p></o:p></p>
<p>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></p>
<p>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></p>
</div>
</body>
</html>
<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> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>