Maybe like this then sorry for the large amount of mails...<br><br><div class="gmail_quote">On Tue, Feb 2, 2010 at 12:40 PM, Hanneke Van Dijk <span dir="ltr"><<a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de">Hanneke.vanDijk@med.uni-duesseldorf.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Arjen,<br>
<br>
This time I am plotting cortico-muscular coherence obtained from ft_freqanalysis_mtmfft with fourier output and then using ft_connectivityanalysis. I wanted to plot the coherence on helmet-level only for 8-12 Hz. I attached the figures; When I do the average over the .cohspctrm field myself (or add the line I reported before) I get the left plot (figure 2) and if I say cfg.xlim I get the right plot (figure 1).<br>
<br>
Groetjes Hanneke<br>
<div class="im"><br>
<br>
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Institut für Klinische Neurowissenschaften und Medizinische Psychologie<br>
Gebäude-Nr.: 23.02<br>
Ebene: 03 Zimmer-Nr.: 47<br>
Tel.: 0211-81-13074<br>
Mail : <a href="mailto:hanneke.vandijk@med.uni-duesseldorf.de">hanneke.vandijk@med.uni-duesseldorf.de</a><br>
<a href="http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html" target="_blank">http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html</a><br>
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<br>
<br>
</div>-----Ursprüngliche Nachricht-----<br>
Von: FieldTrip discussion list im Auftrag von <a href="mailto:a.stolk@fcdonders.ru.nl">a.stolk@fcdonders.ru.nl</a><br>
Gesendet: Di 02.02.2010 12:03<br>
An: <a href="mailto:FIELDTRIP@NIC.SURFNET.NL">FIELDTRIP@NIC.SURFNET.NL</a><br>
Betreff: Re: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127<br>
<div><div></div><div class="h5"><br>
Hi Hanneke,<br>
<br>
Thank you for your report. Could you specify some more details to help locating the problem?<br>
<br>
Are you trying to plot event-related fields or components (I'm asking this because of our earlier mail exchanges)? For the latter, I could recommend the ft_topoplotIC function. This one has maxmin values for the z-axis by default, but is more intuitive.<br>
<br>
An example:<br>
<br>
cfg = [];<br>
cfg.layout = 'NM122_ver.lay';<br>
cfg.component = 1;<br>
ft_topoplotIC(cfg,comp);<br>
<br>
<br>
Best,<br>
Arjen<br>
<br>
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----- Original Message -----<br>
From: "Hanneke Van Dijk" <<a href="mailto:Hanneke.vanDijk@MED.UNI-DUESSELDORF.DE">Hanneke.vanDijk@MED.UNI-DUESSELDORF.DE</a>><br>
To: <a href="mailto:FIELDTRIP@NIC.SURFNET.NL">FIELDTRIP@NIC.SURFNET.NL</a><br>
Sent: Tuesday, February 2, 2010 11:16:40 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna<br>
Subject: [FIELDTRIP] BUG in ft_topoplotER (cfg.xlim) version 20100127<br>
<br>
Dear all,<br>
<br>
I wanted to report a bug in ft_topoplotER (Fieldtrip version 20100127), regarding the use of cfg.xlim. It doesn't seem to use cfg.xlim when you choose one, but just to use the 'maxmin'. When I average the data over xlim myself I get a completely different topoplot then when I use cfg.xlim for the same range. I wouldn't have known if I didn't need to average over xlim for other reasons.<br>
<br>
It seems to happen between lines 445 and 452. The data are selected for cfg.ylim and cfg.component but not for cfg.xlim. This changes the outlook on my data completely, and I think this could be important for all users of this version. Therefore I send it to the entire mailing list.<br>
<br>
I have changed it now to:<br>
444 % make dat structure with one value for each channel<br>
445 dat = getsubfield(data, cfg.zparam);<br>
446 if ~isempty(cfg.yparam),<br>
447 dat = dat(:, ymin:ymax, xmin:xmax);<br>
448 dat = nanmean(nanmean(dat, 2), 3);<br>
449 elseif ~isempty(cfg.component) | ~isempty(cfg.xlim);%this part Hanneke added<br>
450 dat = dat(:, xmin:xmax);<br>
451 dat = nanmean(dat, 2);<br>
452 end<br>
453<br>
454 dat = dat(:);<br>
<br>
This helps for me and it is very important for me as well, my data looks meaningfull now!<br>
<br>
Best and good luck!<br>
<br>
Hanneke<br>
<br>
<br>
<br>
<br>
--------------------------------------------------<br>
Institut für Klinische Neurowissenschaften und Medizinische Psychologie<br>
Gebäude-Nr.: 23.02<br>
Ebene: 03 Zimmer-Nr.: 47<br>
Tel.: 0211-81-13074<br>
Mail : <a href="mailto:hanneke.vandijk@med.uni-duesseldorf.de">hanneke.vandijk@med.uni-duesseldorf.de</a><br>
<a href="http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html" target="_blank">http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html</a><br>
<br>
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----------------------------------<br>
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 href="http://listserv.surfnet.nl/archives/fieldtrip.html" target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a> and <a href="http://www.ru.nl/neuroimaging/fieldtrip" target="_blank">http://www.ru.nl/neuroimaging/fieldtrip</a>.<br>
<br>
----------------------------------<br>
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 href="http://listserv.surfnet.nl/archives/fieldtrip.html" target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a> and <a href="http://www.ru.nl/neuroimaging/fieldtrip" target="_blank">http://www.ru.nl/neuroimaging/fieldtrip</a>.<br>
<br>
</div></div>figure;<br>
cfgp=[];<br>
cfgp.cohrefchannel = {'MEG063+064'};<br>
cfgp.xparam = 'freq';<br>
cfgp.zparam = 'cohspctrm';<br>
cfgp.layout = 'NM122combined_test.lay';<br>
cfgp.showlabels = 'yes';<br>
cfgp.xlim = [8 12];<br>
%cfgp.zlim = [0 1];<br>
ft_topoplotER(cfgp,fd_ccc_off);colorbar<br>
<div><div></div><div class="h5"><br>
<br>
----------------------------------<br>
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 href="http://listserv.surfnet.nl/archives/fieldtrip.html" target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a> and <a href="http://www.ru.nl/neuroimaging/fieldtrip" target="_blank">http://www.ru.nl/neuroimaging/fieldtrip</a>.<br>
</div></div></blockquote></div><br>
<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>