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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Roemer,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks a lot. My previous
version worked with your proposed corrections and I downloaded the new version
today. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Sorry, I have yet another
question, this time regarding the parameters controlling statistical analysis
for the cluster-based test statistic.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>When asking myself
whether it made sense to set cfg.testtail and cfg.tail independently, I found
the error message in clusterstat.m, l.32, which states that the parameters should
be equal. Could you perhaps mention this requirement in the tutorials?<o:p></o:p></span></font></p>
<h1><b><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial;color:navy;font-weight:normal'>Also, regarding
cfg.alpha and cfg.clusteralpha – just to make sure that I have got things
right: For a two-sided test, I have to split cfg.alpha manually so as to equal
half the desired significance level but I do not have to change cfg.clusteralpha
explicitly, is this correct? I gathered so from the tutorials and it looks so
from the code (in clusterstat and the statfun functions, the alpha parameter is
halved automatically). If nothing is specified, both parameters are set to 0.05.
As a two-sided test is the default, does this mean that the false alarm rate is
set at the 10% level if the user does not specify anything, or have I
overlooked something? (I have to admit that I am impressed with the intricacies
but that I have not really grasped the details…)<o:p></o:p></span></font></b></h1>
<h1><b><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial;color:navy;font-weight:normal'>By the way, the
tutorial <a name="cluster-based_permutation_tests_on_event">on c</a></span></font></b><font
size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy;font-weight:normal'>luster-based permutation tests
on event related fields</span></font><font size=2 color=navy face=Arial><span
lang=EN-GB style='font-size:10.0pt;font-family:Arial;color:navy;font-weight:
normal'> mentions a parameter cfg.alphathresh, which I only found in the clusterrand
functions and which I took to mean cfg.clusteralpha.<o:p></o:p></span></font></h1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>All the best to all of
you<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Andrea<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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lang=EN-GB style='font-size:12.0pt'><o:p> </o:p></span></font></p>
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lang=EN-GB style='font-size:12.0pt'> </span></font><font size=2
face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold'>From:</span></font></b><font
size=2 color=black face=Tahoma><span lang=EN-US style='font-size:10.0pt;
font-family:Tahoma;color:windowtext'> <st1:PersonName w:st="on">FieldTrip
discussion list</st1:PersonName> [mailto:FIELDTRIP@NIC.SURFNET.NL] <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
14:08<br>
<b><span style='font-weight:bold'>To:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [FIELDTRIP] Warning
in ft_topoplotER</span></font><font color=black><span lang=EN-US
style='color:windowtext'><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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: <o:p></o:p></span></font></p>
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</xml><![endif]--></u1:SmartTagType>Dear Roemer,<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>thanks a lot for your
help and the time you are taking to assist me! Your remarks have been really
helpful. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>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. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>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.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>The warning is<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Warning: cfg.highlight is
now used for specifing highlighting-mode, use cfg.highlightchannel instead of
cfg.highlight for specifiying channels<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>> In ft_topoplotER at
214<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'> In topoplotER at 17<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'> In ft_clusterplot
at 277<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'> In
test_clusterplot at 5<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks a lot!<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Best regards<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Andrea<u1:p></u1:p></span></font><o:p></o:p></p>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
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<u1:p></u1:p>
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<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold'>From:</span></font></b><font
size=2 color=black face=Tahoma><span lang=EN-US style='font-size:10.0pt;
font-family:Tahoma;color:windowtext'> <st1:PersonName u4:st="on"><st1:PersonName
w:st="on">FieldTrip discussion list</st1:PersonName></st1:PersonName> [<a
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
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><o:p></o:p></p>
</div>
<u1:p></u1:p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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>
<br>
<o:p></o:p></span></font></p>
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<p><font size=3 color=black face="Times New Roman"><span style='font-size:12.0pt'>The
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<p><font size=3 color=black face="Times New Roman"><span style='font-size:12.0pt'>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.<o:p></o:p></span></font></p>
<p><font size=3 color=black face="Times New Roman"><span style='font-size:12.0pt'><a
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<pre><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>-- <o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Roemer van der Meij MSc<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Scientific Programmer & Data-Analyst<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Donders Institute for Brain, Cognition and Behaviour<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Centre for Cognition<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>P.O. Box 9104<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>6500 HE Nijmegen<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>The Netherlands<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Tel: +31(0)24 3612631 <o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>E-mail: <a
href="mailto:r.vandermeij@donders.ru.nl">r.vandermeij@donders.ru.nl</a><o:p></o:p></span></font></pre>
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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> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</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> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>