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Hi Gregor,<br>
<br>
that sounds indeed odd - although I am glad that I did not mess up
something in prepare_neighbours ;) <br>
However, when I look at the code, it seems that channeighbstructmat
will only be used when ~issource, and the call to the spm function
will only be when issource, so I cannot see a direct relation
between these two. Could you provide some more information, e.g. in
what line and function you observed the call to the spm function? If
you like you could also create a bugreport on
<a class="moz-txt-link-freetext" href="http://bugzilla.fcdonders.nl/">http://bugzilla.fcdonders.nl/</a> for this. In any case, one of us will
then tackle your problem as soon as possible and try to solve it. I
hope that we can reproduce your bug here, else we might ask for a
snippet of your data/workspace.<br>
<br>
Thanks in any case for having a precise look at what is going on!<br>
<br>
Best,<br>
Jörn<br>
<br>
On 11/11/2011 6:08 PM, Gregor Volberg wrote:
<blockquote
cite="mid:4EBD64B2020000570000B793@gwsmtp1.uni-regensburg.de"
type="cite">
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">Hi Jörn,</font> </p>
<br>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">thanks a lot for your response. I meanwhile checked
some possible reasons for the different clusterings and I am
coming closer. </font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">I could reproduce the described error with two
different datasets (62 channel and 29 channel EEG), on two
different computers and with two different versions of
fieldtrip (2011 versions). First of all, I checked the
neighbourhood structures. They are identical in my two
analyses - same number of electrodes, same order, same
neighbours. I checked that before and after entering
neighbours into the analyses (by comparing the
stat.cfg.neighbours) - they are the same.</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">I then searched through the code and found the
channeighbstructmat that is constructed during the call of
"clusterstat.m". I saved these matrices during the call of
ft_freqstatistics and found that, with the same neighbourhood
structures, the channeighbstructmat looked completely
different in the old and new version. I then changed the code
of the new FT "clusterstat.m" so that it reads in the
channeighbstructmat obtained with the old FT version - then
everything works perfect.</font> </p>
<br>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">Thus, the problem is most likely an incorrect
channeighbstructmat. I figured out that in my case, FT calls
an SPM8 function spm_bwlabeln during construction of the
channeighbstructmat, which older version do not do. However,
if I understood the code correctly, the SPM function should
only be called for source data?! Could it be that, because my
data is a 4D grand-average structure ( dimord:
'subj_chan_freq_time'), FT assumes source data?</font> </p>
<br>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">Thanks again for your help,</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2">Gregor</font> </p>
<br>
<p style="margin-bottom: 0; margin-top: 0"> <font face="Dialog"
size="2"> </font><br>
<br>
<font style="font-size: 10pt" face="Dialog"><br>
--
<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%0D">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
</a><br>
<br>
<br>
</font>>>> "Jörn M.
Horschig"<a class="moz-txt-link-rfc2396E" href="mailto:jm.horschig@donders.ru.nl"><jm.horschig@donders.ru.nl></a> 11/9/2011 4:00 PM
>>><br>
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: </p>
<blockquote type="cite"
cite="mid:362958968.59435.1320335856835.JavaMail.fmail@mwmweb078">
<p style="margin-bottom: 0; margin-top: 0"> 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>
</p>
<blockquote style="margin-left: 5px; padding-left: 5px;
border-left: 2px solid blue; padding-top: 5px">
<p style="margin-bottom: 0; margin-top: 0"> </p>
<hr> <b>Von:</b> "Gregor Volberg" <a moz-do-not-send="true"
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 moz-do-not-send="true"
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="font-variant: normal; margin-right: 4px;
line-height: normal; margin-left: 4px; margin-top: 4px;
margin-bottom: 1px">
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">Dear fieldtrip community,</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <br>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <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>
<p style="margin-bottom: 0; margin-top: 0"> <br>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <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: 0; margin-top: 0"> <font
face="Dialog" size="2"> </font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <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>
<p style="margin-bottom: 0; margin-top: 0"> <br>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <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>
<p style="margin-bottom: 0; margin-top: 0"> <br>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">Best regards,</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">Gregor</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <br>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg = [];</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.neighbours = neighbours;</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.minnbchan=1;</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.avgoverfreq = 'yes';</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.avgovertime = 'yes';</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.method = 'montecarlo';</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.correctm = 'cluster';</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.statistic =
'depsamplesT';</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.tail = 0;</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.alpha = 0.05;</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.clusteralpha = 0.05;</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.numrandomization = 1000;</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <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: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.uvar = 1;</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.ivar = 2;</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.latency = [2.24 2.53];</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">cfg.frequency = [17 21];%</font>
</p>
<p style="margin-bottom: 0; margin-top: 0"> <font
face="Dialog" size="2">stat = ft_freqstatistics(cfg, DC,
TC);</font> </p>
<p style="margin-bottom: 0; margin-top: 0"> <br>
<span style="style="font-size: 10pt"
FONT-FAMILY:"Dialog"
;FONT-SIZE:"10pt"">--<br style="font-size:
10pt; font-family: Dialog">
Dr. rer. nat. Gregor Volberg <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:gregor.volberg@psychologie.uni-regensburg.de"><gregor.volberg@psychologie.uni-regensburg.de></a> (
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="mailto:gregor.volberg@psychologie.uni-regensburg.de">mailto:gregor.volberg@psychologie.uni-regensburg.de</a> )<br
style="font-size: 10pt; font-family: Dialog">
University of Regensburg<br style="font-size: 10pt;
font-family: Dialog">
Institute for Experimental Psychology<br
style="font-size: 10pt; font-family: Dialog">
93040 Regensburg, Germany<br style="font-size: 10pt;
font-family: Dialog">
Tel: +49 941 943 3862<br style="font-size: 10pt;
font-family: Dialog">
Fax: +49 941 943 3233<br style="font-size: 10pt;
font-family: Dialog">
<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></span><br>
<br>
</p>
</div>
</blockquote>
<p style="margin-bottom: 0; margin-top: 0"> <br>
</p>
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</blockquote>
<p style="margin-bottom: 0; margin-top: 0">
<br>
<br>
</p>
<pre class="moz-signature" cols="72"><p style="white-space: pre; margin-top: 0; margin-bottom: 0" class="moz-signature" cols="72">
-- </p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Jörn M. Horschig</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
PhD Student</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Donders Institute for Brain, Cognition and Behaviour </p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Centre for Cognitive Neuroimaging</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Radboud University Nijmegen </p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Neuronal Oscillations Group</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
P.O. Box 9101</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
NL-6500 HB Nijmegen</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
The Netherlands</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Contact:</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
E-Mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a></p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Tel: +31-(0)24-36-68493</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Web: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a></p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Visiting address:</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Trigon, room 2.30</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
Kapittelweg 29</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
NL-6525 EN Nijmegen</p>
<p style="white-space: pre; margin-bottom: 0; margin-top: 0">
The Netherlands</p>
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<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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