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Hi Tobias,<br>
<br>
thank you very much for tracking this down. I encountered a similar
issue in ft_channelrepair a few months ago - some built-in
Matlab-functions rearrange a cell-array of string alphabetically. <br>
I'm gonna look into this now and also try to find out in which
revision this lead to a problem.<br>
<br>
Best,<br>
Jörn<br>
<br>
On 11/23/2011 7:08 PM, Tobias Staudigl wrote:
<blockquote cite="mid:4ECD36AF.6000806@uni-konstanz.de" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
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 moz-do-not-send="true"
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>
</div>
</blockquote>
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</p>
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<br>
</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>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Visiting address:</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
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<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
Kapittelweg 29</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
NL-6525 EN Nijmegen</p>
<p style="MARGIN-TOP: 0px; WHITE-SPACE: pre; MARGIN-BOTTOM: 0px">
The Netherlands</p>
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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 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>
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<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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<pre wrap="">_______________________________________________
fieldtrip mailing list
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>
<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
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<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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