Warning in ft_topoplotER

Wed Jan 20 14:07:45 CET 2010

Hi Andrea,

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.

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).

Thanks for pointing out these bugs!

Best,
Roemer

Andrea Ostendorf wrote:
>
> Dear Roemer,
>
>
>
> thanks a lot for your help and the time you are taking to assist me!
> Your remarks have been really helpful.
>
>
>
> 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.
>
>
>
> 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.
>
>
>
> The warning is
>
> Warning: cfg.highlight is now used for specifing highlighting-mode,
> use cfg.highlightchannel instead of cfg.highlight for specifiying channels
>
> > In ft_topoplotER at 214
>
>   In topoplotER at 17
>
>   In ft_clusterplot at 277
>
>   In test_clusterplot at 5
>
>
>
> Thanks a lot!
>
>
>
> Best regards
>
> Andrea
>
>
>
> ------------------------------------------------------------------------
>
> *From:* FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> *On Behalf Of *Roemer van der Meij
> *Sent:* Mittwoch, 20. Januar 2010 12:52
> *To:* FIELDTRIP at NIC.SURFNET.NL
> *Subject:* Re: [FIELDTRIP] Thanks / warning in ft_topoplotER
>
>
>
> Hi Andrea,
>
> Always happy to help. And thank you for helping us squashing bugs!
>
> 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!
>
> 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.
>
> 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.
> I copy-pasted it here for easy reference:
> ***********
> % It is possible to use multiple highlight-selections (e.g.: multiple
> statistical clusters of channels)
> % To do this, all the content of the highlight-options (including
> cfg.highlight) should be placed in a cell-array
> % (even if the normal content was already in a cell-array). Specific
> marker settings (e.g. color, size) are defaulted when
> % not present.
> % Example (3 selections):
> % cfg.highlight               = {'labels', 'labels', 'numbers'}
> % cfg.highlightchannel    = {{'MZF03','MZC01','MRT54'}, [1:5], 'C*'}
> % cfg.highlightsymbol    = {'o',[],'+'}          % the empty option
> will be defaulted
> % cfg.highlightcolor       = {'r',[0 0 1]};      % the missing option
> will be defaulted
> % cfg.highlightsize         = [];                      % will be set
> to default, as will the missing cfg.highlightfontsize
> ***********
>
> 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.
>
>
> 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 = [];
>
>
> I hope all of the above helps. Thanks for bringing these bugs to our
> attention!
>
> Kind regards,
>
> Roemer
>
>
>
>
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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.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>
> ----------------------------------
>
> 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.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>

--
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: r.vandermeij at donders.ru.nl

----------------------------------
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 http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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