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Hi Gregor,<br>
<br>
did you check your neighbourselection? Maybe something is going
wrong there, given that a lot in this code has changed since 2010.
Could you check that using ft_neighbourplot? This would be the most
logical explanation why the results differ. It does not really make
sense that these three sensors form one cluster, because they should
not be neighbours of each other. So i would suppose that something
is going wrong there.<br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 11/3/2011 4:57 PM, Michael Wibral wrote:
<blockquote
cite="mid:362958968.59435.1320335856835.JavaMail.fmail@mwmweb078"
type="cite">Hi Gregor,<br>
<br>
in principle the first level statistics that determine cluster
membership (and thereby cluster shapes etc.) can also vary from
one set of permutations to the next, esp. on the borders of a
cluster (this is why it is typically said that the localization of
a cluster is not as trustworthy as its existence). Other resaons
for differences are differing number of permutations - did you set
everything the same?<br>
<br>
This said there might well be another problem - I hope the cluster
people can have a look into it.<br>
<br>
Best ,<br>
Michael<br>
<br>
<br>
<blockquote style="border-left: 2px solid blue; margin-left: 5px;
padding-left: 5px; padding-top: 5px;">
<hr><b>Von:</b> "Gregor Volberg"
<a class="moz-txt-link-rfc2396E" href="mailto:Gregor.Volberg@psychologie.uni-regensburg.de"><Gregor.Volberg@psychologie.uni-regensburg.de></a><br>
<b>Gesendet:</b> Nov 2, 2011 6:34:43 PM<br>
<b>An:</b> <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<b>Betreff:</b> [FieldTrip] Wrong clustering of electrodes in
newer FT versions?<br>
<br>
<div style="margin: 4px 4px 1px; line-height: normal;
font-variant: normal;">
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">Dear fieldtrip community,</font></p>
<br>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">I just encountered an unexpected
behavior of FT that I would like to share with the list.
It is that the cluster permutation test formed incorrect
clusters from a given set of significant electrodes in
newer FT versions (ft-20111012; I also tried with
ft-20111028). </font></p>
<br>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">For example, when using an old ft
version (ft-20100810) and freqstatistics I get a negative
cluster with 17 contiguous electrodes. With the newer ft
version, using the same data and the same cfg, three
significant electrodes that are spatially contiguous to
the other significant electrodes are not included in the
cluster. Also, three electrodes that are spatially
seperated and are actually part of the first cluster are
grouped into a separate cluster. I attached a picture
with the respective clusterplots where differences are
marked with red arrows.</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2"> </font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">I am aware that the permutation
p-value for a given cluster can be different in two
separate analyses, but the grouping of significant
electrodes into clusters should always be the same, am i
right? I double-checked the cfg.neighbours, after
conversion to new 'struct' style, and they were identical
in the "old ft" and "new ft" analysis. Also, the
stat.stat field and the stat.cfg.clustercritval were the
same for both analyses. Thus, the same neighbourhood
relations and the same significant electrodes should be
used for grouping. Yet I get different results... </font></p>
<br>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">I am almost sure that this is
trivial, but I could not yet replicate my old results with
new FT and this makes me nervous. Has someone made a
similar experience? Or do newer versions of ft use some
further information besides cfg.neighbours for clustering,
somewhere in the *cfg.previuous perhaps, that I am not
aware of? Any comments are highly welcome.</font></p>
<br>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">Best regards,</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">Gregor</font></p>
<br>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg = [];</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.neighbours = neighbours;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.minnbchan=1;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.avgoverfreq = 'yes';</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.avgovertime = 'yes';</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.method = 'montecarlo';</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.correctm = 'cluster';</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.statistic = 'depsamplesT';</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.tail = 0;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.alpha = 0.05;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.clusteralpha = 0.05;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.numrandomization = 1000;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.design = [[1:14 1:14];
[zeros(1,14)+1 zeros(1,14)+2]];</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.uvar = 1;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.ivar = 2;</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.latency = [2.24 2.53];</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">cfg.frequency = [17 21];%</font></p>
<p style="margin-bottom: 0pt; margin-top: 0pt;"><font
face="Dialog" size="2">stat = ft_freqstatistics(cfg, DC,
TC);</font></p>
<br>
<font style="font-size: 10pt;" face="Dialog">--<br>
Dr. rer. nat. Gregor Volberg
<a class="moz-txt-link-rfc2396E" href="mailto:gregor.volberg@psychologie.uni-regensburg.de"><gregor.volberg@psychologie.uni-regensburg.de></a> (
<a class="moz-txt-link-freetext" href="mailto:gregor.volberg@psychologie.uni-regensburg.de">mailto:gregor.volberg@psychologie.uni-regensburg.de</a> )<br>
University of Regensburg<br>
Institute for Experimental Psychology<br>
93040 Regensburg, Germany<br>
Tel: +49 941 943 3862<br>
Fax: +49 941 943 3233<br>
<a moz-do-not-send="true"
href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html%0A">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
</a></font><br>
<br>
</div>
</blockquote>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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