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Hi Gregor and Jörn, <br>
<br>
I find a simliar problem in my data (bti148). <br>
2 sets of channels that share no connections across the sets are
included in one cluster. <br>
<br>
I am not sure, whether spm_bwlabel is the actual problem. However, I
do not really understand why calling that function would be
necessary. <br>
FT calls the function spm_bwlabel during findcluster.m, line 95.
(findcluster.m is called by clusterstat.m).<br>
As far as I understand, spm_bwlabel is similar to bwlabel.m which
searches for connected bins in a matrix. <br>
The input to spm_label is the vector 'onoff' (in may case :148x1
logical), which already contains information about neighboring
channels. <br>
Searching for connected bins in this vector does seem odd to me. <br>
<br>
However, I supsect something else to be the reason for the wrong
clustering, at least in my data. <br>
In line 166, ft_freqstatistics.m changes the order of the channel
labels:<br>
<br>
chan = intersect(chan, varargin{i}.label);<br>
<br>
Original order: {'A68'; 'A58'; 'A148';...}<br>
Re-arranged in 'chan': {'A1';'A10';'A100'; 'A101'; 'A102';...}<br>
<br>
in line 193, ft_freqstatistics calls:<br>
cfg.channel = ft_channelselection(cfg.channel, chan);<br>
<br>
now cfg.channel contains the re-aranged order. <br>
On the basis of cfg.channel, the 'channeighbstructmat' is computed
by makechanneighbstructmat(cfg) in clusterstat.m.<br>
The statistics on the data is computed without re-arranging the
channels in statfun_depsamplesT.m ('statobs').<br>
In findcluster.m, line 84 (called during clusterstat.m, l. 197), the
matrices 'onoff' and 'selectmat' are multiplied. <br>
To my understanding, 'onoff' is based on the statistics that is
computed with the originial channel order. <br>
'selectmat' is based on the re-arranged order. <br>
If true, the multiplication of these matrices is wrong. <br>
<br>
Hope this helps, although I might have missed something obvious and
might be totally wrong then. <br>
<br>
best, <br>
tobias<br>
<br>
<br>
Am 14.11.2011 17:46, schrieb Gregor Volberg:
<blockquote
cite="mid:4EC153F2020000570000B7F0@gwsmtp1.uni-regensburg.de"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<meta name="GENERATOR" content="MSHTML 8.00.6001.19154">
<div>Hi Jörn,</div>
<div> </div>
<div>yes, sure I can provide you with some more information. I
hope to do so due Wednesday.</div>
<div>Thanks a lot again for your kind support!</div>
<div>Gregor</div>
<div> </div>
<div> </div>
<div>-- <br>
Dr. rer. nat. Gregor Volberg <<a moz-do-not-send="true"
href="mailto:gregor.volberg@psychologie.uni-regensburg.de">gregor.volberg@psychologie.uni-regensburg.de</a>>
( <a moz-do-not-send="true"
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">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html</a><br>
<br>
<br>
>>> "Jörn M. Horschig"<a class="moz-txt-link-rfc2396E" href="mailto:jm.horschig@donders.ru.nl"><jm.horschig@donders.ru.nl></a>
14.11.2011 09:51 >>><br>
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 moz-do-not-send="true"
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: </div>
<blockquote
cite="mid:4EBD64B2020000570000B793@gwsmtp1.uni-regensburg.de"
type="cite">
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">Hi Jörn,</font> </p>
<br>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">Thanks again for your help,</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">Gregor</font> </p>
<br>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
<br>
<font style="FONT-SIZE: 10pt" face="Dialog"><br>
-- <br>
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>
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
href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html%0D"
moz-do-not-send="true">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
</a><br>
<br>
<br>
</font>>>> "Jörn M. Horschig"<a
moz-do-not-send="true" 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
cite="mid:362958968.59435.1320335856835.JavaMail.fmail@mwmweb078"
type="cite">
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px">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="BORDER-LEFT: blue 2px solid; PADDING-LEFT:
5px; MARGIN-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"
moz-do-not-send="true"><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"
moz-do-not-send="true">fieldtrip@donders.ru.nl</a><br>
<b>Betreff:</b> [FieldTrip] Wrong clustering of electrodes
in newer FT versions?<br>
<br>
<div style="LINE-HEIGHT: normal; FONT-VARIANT: normal;
MARGIN: 4px 4px 1px">
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">Dear fieldtrip community,</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><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-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">Best regards,</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">Gregor</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg = [];</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.neighbours = neighbours;</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.minnbchan=1;</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.avgoverfreq = 'yes';</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.avgovertime = 'yes';</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.method =
'montecarlo';</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.correctm = 'cluster';</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.statistic =
'depsamplesT';</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.tail = 0;</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.alpha = 0.05;</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.clusteralpha = 0.05;</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.numrandomization = 1000;</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.design = [[1:14 1:14];
[zeros(1,14)+1 zeros(1,14)+2]];</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.uvar = 1;</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.ivar = 2;</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.latency = [2.24
2.53];</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">cfg.frequency = [17 21];%</font>
</p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><font
face="Dialog" size="2">stat = ft_freqstatistics(cfg,
DC, TC);</font> </p>
<p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><br>
<span style="FONT-SIZE: 10pt; style: 'font-size: 10pt'
FONT-FAMILY:'Dialog'">--<br style="FONT-FAMILY:
Dialog; FONT-SIZE: 10pt">
Dr. rer. nat. Gregor Volberg <a
class="moz-txt-link-rfc2396E"
href="mailto:gregor.volberg@psychologie.uni-regensburg.de"
moz-do-not-send="true"><gregor.volberg@psychologie.uni-regensburg.de></a> (
<a class="moz-txt-link-freetext"
href="mailto:gregor.volberg@psychologie.uni-regensburg.de"
moz-do-not-send="true">mailto:gregor.volberg@psychologie.uni-regensburg.de</a> )<br
style="FONT-FAMILY: Dialog; FONT-SIZE: 10pt">
University of Regensburg<br style="FONT-FAMILY:
Dialog; FONT-SIZE: 10pt">
Institute for Experimental Psychology<br
style="FONT-FAMILY: Dialog; FONT-SIZE: 10pt">
93040 Regensburg, Germany<br style="FONT-FAMILY:
Dialog; FONT-SIZE: 10pt">
Tel: +49 941 943 3862<br style="FONT-FAMILY: Dialog;
FONT-SIZE: 10pt">
Fax: +49 941 943 3233<br style="FONT-FAMILY: Dialog;
FONT-SIZE: 10pt">
<a
href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html%0A"
moz-do-not-send="true">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
</a></span><br>
<br>
</p>
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</blockquote>
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</p>
<pre class="moz-signature" cols="72"><p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px" class="moz-signature" cols="72">
-- </p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Jörn M. Horschig</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
PhD Student</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Donders Institute for Brain, Cognition and Behaviour </p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Centre for Cognitive Neuroimaging</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Radboud University Nijmegen </p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Neuronal Oscillations Group</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
P.O. Box 9101</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
NL-6500 HB Nijmegen</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
The Netherlands</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Contact:</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl" moz-do-not-send="true">jm.horschig@donders.ru.nl</a></p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Tel: +31-(0)24-36-68493</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders" moz-do-not-send="true">http://www.ru.nl/donders</a></p>
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Visiting address:</p>
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<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
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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 moz-do-not-send="true" 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 moz-do-not-send="true" 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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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Tobias Staudigl
Fachbereich Psychologie - ZPR
Postfach ZPR
78457 Konstanz
ZPR, Haus 12
Tel.: +49 (0)7531 / 88 - 5703
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