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Hi Andrea,<br>
<br>
Thanks for the data/script, it was exactly what I needed. There was a
silly bug in ft_clusterplot where several calls to cfg.highlight were
not changed to cfg.highlightchannel during the big update, and I failed
to notice them during browsing. Things should be fixed now (will be on
the ftp-server tonight). You can fix it in your own version easily by
changing in line 267 and line 285 cfg.highlight >>>
cfg.highlightchannel. Clusterplot should work as intended afterwards. <br>
<br>
I also realised now that any additional options that go into
clusterplot will not be used (like cfg.marker), these are fixed now as
well (on ftp-server tonight).<br>
<br>
Thanks for pointing out these bugs!<br>
<br>
Best,<br>
Roemer<br>
<br>
<br>
<br>
Andrea Ostendorf wrote:
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<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Dear Roemer,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">thanks
a lot for your
help and the time you are taking to assist me! Your remarks have been
really
helpful. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">The
warning is from
topoplotER, which I call indirectly through ft_clusterplot. Thanks for
pointing
out that I am not to use the options directly. I saw some options in
the help
of ft_clusterplot together with the hint that more options were to be
found in
topoplotER. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Since
I keep having
trouble with uploading files to your server, I attach a test MATLAB
file
(stripped down to the basics) and my data. I hope that is okay, it is
really
quite a small amount of data. Otherwise, I would try my private Ubuntu
computer.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">The
warning is<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Warning:
cfg.highlight is
now used for specifing highlighting-mode, use cfg.highlightchannel
instead of
cfg.highlight for specifiying channels<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">>
In ft_topoplotER at
214<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">
In topoplotER at 17<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">
In ft_clusterplot at
277<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">
In test_clusterplot at
5<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Thanks
a lot!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Best
regards<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Andrea<o:p></o:p></span></font></p>
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style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
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<p class="MsoNormal"><b><font color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; color: windowtext; font-weight: bold;"
lang="EN-US">From:</span></font></b><font color="black" face="Tahoma"
size="2"><span
style="font-size: 10pt; font-family: Tahoma; color: windowtext;"
lang="EN-US"> <st1:PersonName w:st="on">FieldTrip discussion list</st1:PersonName>
[<a class="moz-txt-link-freetext" href="mailto:FIELDTRIP@NIC.SURFNET.NL">mailto:FIELDTRIP@NIC.SURFNET.NL</a>] <b><span style="font-weight: bold;">On
Behalf Of </span></b>Roemer van der Meij<br>
<b><span style="font-weight: bold;">Sent:</span></b> Mittwoch, 20.
Januar 2010
12:52<br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:FIELDTRIP@NIC.SURFNET.NL">FIELDTRIP@NIC.SURFNET.NL</a><br>
<b><span style="font-weight: bold;">Subject:</span></b> Re:
[FIELDTRIP] Thanks /
warning in ft_topoplotER</span></font><font color="black"><span
style="color: windowtext;" lang="EN-US"><o:p></o:p></span></font></p>
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<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">Hi Andrea,<br>
<br>
Always happy to help. And thank you for helping us squashing bugs!<br>
<br>
Are you sure you are using the most recent fieldtrip version? There was
a bug
several weeks ago that gave the warning (which used to be on line 214,
but is
now on line 215) even when cfg.highlight was not numerical. (if it's
numerical,
it is assumed cfg.highlight is used in the old way). If you have a
version that
is newer than 19-12-2009 (date of previous bug fix), could you post the
exact
code you use to call ft_topoplotER? This could give me a better idea on
where
in the code the problem lies. Could you then also post the exact
warning matlab
spits out? (if it's not a version problem, something complicated is
going on
and all information is helpful). Thanks!<br>
<br>
Concerning ft_clusterplot, you're not actually supposed to use the
highlighting
options directly. As clusterplot tries to determine the clustering
automatically, this could possibly interfere with it's normal
functioning.
Thanks for pointing this out. I now added a check for these 'forbidden'
options
and they will be removed automatically. The updated clusterplot will be
uploaded to the ftp-server somewhere late in the evening today. <br>
<br>
However, if you want to manage you're own clustering directly, you can
also do
this using topoplotER/TFR. It might be a bit difficult, but you have to
put all
the highlighting options in its own cell (including the ones that were
already
in cells). There is 'hidden' documentation about this in topoplotER
(you won't
see it with the help/doc command, but you will if you edit the
function), you
can find it just below the normal documentation.<br>
I copy-pasted it here for easy reference:<br>
***********<br>
% It is possible to use multiple highlight-selections (e.g.: multiple
statistical clusters of channels)<br>
% To do this, all the content of the highlight-options (including
cfg.highlight) should be placed in a cell-array<br>
% (even if the normal content was already in a cell-array). Specific
marker
settings (e.g. color, size) are defaulted when<br>
% not present. <br>
% Example (3 selections):<br>
% cfg.highlight
= {'labels', 'labels', 'numbers'}<br>
% cfg.highlightchannel = {{'MZF03','MZC01','MRT54'}, [1:5], 'C*'}<br>
% cfg.highlightsymbol = {'o',[],'+'}
% the empty option will be defaulted<br>
% cfg.highlightcolor = {'r',[0 0
1]}; % the missing option will be defaulted<br>
% cfg.highlightsize =
[];
% will be set to default, as will the missing
cfg.highlightfontsize<br>
***********<br>
<br>
Using these options you should be able to get the same individual plots
clusterplot can give you. If you do not want to see the other channels,
set
cfg.marker = 'off';. On the use of the different routines, topoplotTFR
is
identical to topoplotER, but is just present because of our present
naming-scheme.
Clusterplot however, is a wrapper around topoplotER/TFR designed to
quickly and
without much configuring plot your statistical clusters (which requires
statistics output as input). By using the 'hidden' options above, you
can make
topoplotER/TFR do exactly the same as clusterplot, but then you can
specify
your own clusters.<br>
<br>
<br>
We are currently looking into your question number 3, as it appears
things go a
little deeper there. There are at least some situations where
cfg.neighbours =
[] apparently doesn't work, but we are still figuring out why. For the
moment,
a really ugly and time consuming workaround would be to make a for-loop
over
single channels, but it would prevent the clustering over channels and
should
provide (per channel) the exact same output as cfg.neighbours = [];<br>
<br>
<br>
I hope all of the above helps. Thanks for bringing these bugs to our
attention!<br>
<br>
Kind regards,<br>
<br>
Roemer<br>
<br>
<br>
<o:p></o:p></span></font></p>
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<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> <a class="moz-txt-link-freetext" href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a></p>
<p> <a class="moz-txt-link-freetext" href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a></p>
<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> <a class="moz-txt-link-freetext" href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a></p>
<p> <a class="moz-txt-link-freetext" href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a></p>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Roemer van der Meij MSc
Scientific Programmer & Data-Analyst
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
P.O. Box 9104
6500 HE Nijmegen
The Netherlands
Tel: +31(0)24 3612631
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:r.vandermeij@donders.ru.nl">r.vandermeij@donders.ru.nl</a></pre>
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<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>