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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>
<br>
Andrea Ostendorf wrote:
<blockquote cite="mid:6D7D6970FEC64AE5AE0EF13A14CCFF96@LAT6500Andrea"
type="cite">
<pre wrap="">Dear Roemer, dear Jan-Mathijs,
Thanks for your quick answers! Sorry for getting back so late.
Dear Jan-Mathijs, thanks for the comment on the symbolic links. My
colleagues and I, as well as other BESA users, use Windows at work so it
would be nice to get news on your proposed OS-independent solution.
Dear Roemer, yes, I was referring to ft_topoplotER. I forgot to mention this
although I was aware of the fact. Thanks for the explanations!
I am a bit confused because I still end up with the same warning (line 214
of ft_topoplotER) even if I use
cfg.highlightchannel = 'all'; (or a numerical index vector)
cfg.highlight = 'on';
I used the same setting (with different data) for both ft_topoplotTFR and
ft_clusterplot. Both call topoplotER, although the call looks a bit
different.
There is no problem in the case of ft_topoplotTFR. If I modify
cfg.highlightchannel, I see a change.
When using ft_clusterplot with this same setting, the significant channels
appear to be highlighted but I observe no change upon modification of
cfg.highlightchannel, and I get the warning in ft_topoplotER (line 214).
On debugging, I see that the lines below l.606 in ft_topoplotER
("if ~strcmp(cfg.marker,'off')") are carried out only in my call of
ft_topoplotTFR.
Have I done anything wrong, or are the settings treated differently by both
routines?
Have a nice evening! And thanks a lot to both of you!
All the best
Andrea
</pre>
<blockquote type="cite">
<pre wrap="">2) ft_clusterplot: Since cfg.highlight has changed, I keep getting a
warning
although I have now switched the setting to cfg.highlight = 'on'. Is there
a
possibility to implement something like the following example (taken from
the tutorial on cluster-based permutation tests on event-related fields)?
It looks as if you are referring to ft_topoplotER and not
ft_clusterplot. If that assumption is correct, than you can definitely
use something like:
cfg.highlight = find (pos_int==1|neg_int==-1);
However, cfg.highlight would then need to be changed into
cfg.highlightchannel. In the new highlighting configuration,
cfg.highlight is used to determine highlighting-method (like 'on',
'labels', 'numbers'), while cfg.highlightchannel is meant to indicate
which channels your actually want to highlight. This can be a numerical
index vector (like above), channel-labels, channel-labels with wildcards
and anything else ft_channelselection can take as input.
The tutorial on the wiki hasn't been updated yet to reflect the changes
to topoplotER (I'll do that soon), but the following should work:
cfg.highlight = 'on';
cfg.highlightchannel = find (pos_int==1|neg_int==-1);
(using all the defaults this should mark every channel in
cfg.highlightchannel with a '*' and every other channel with a 'o')
Hope this helps!
Best,
Roemer
</pre>
</blockquote>
<pre wrap=""><!---->
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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. See also <a class="moz-txt-link-freetext" href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a> and <a class="moz-txt-link-freetext" href="http://www.ru.nl/neuroimaging/fieldtrip">http://www.ru.nl/neuroimaging/fieldtrip</a>.
</pre>
</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>