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Dear Jac,
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<div class="">I think that this is caused by the fact that currently (i.e. at some point in time it has been changed) the ft_prepare_layout function scales the spatial distribution of the channels (in your case a subset of the full MEG sensor array) to optimally
fill the silly circle that represents the ‘outline of the head’. This circle is created on the fly.</div>
<div class="">Can you confirm that you don’t have this problem if instead of cfg.layout = ‘CTF275.lay’, you use ‘CTF275_helmet.mat’?</div>
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<div class="">It is great that people still find their way to the ‘crossvalidate’ method in ft_freqstatistics. Allow me to seize the opportunity here to advertise some new functionality (not fully tested yet for frequency domain data, but at least it works
well for time domain channel data) in toolbox for doing multivariate statistics: Matthias Treder has kindly contributed a gateway function to his MVPA-light toolbox (which can be found on github). In FieldTrip, when specifying cfg.method = ‘mvpa’ you will
end up in this gateway function, and it allows for using the awesome functionality of MVPA-light. There’s also a new tutorial on the website that demonstrates how to use it. Check out the ‘news’ section at the home-page of the fieldtrip wiki to get more information.</div>
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<div class="">Thanks,</div>
<div class="">Jan-Mathijs</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
J.M.Schoffelen, MD PhD<br class="">
Associate PI, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<div class="">On 14 Mar 2019, at 10:37, Jac Billington <<a href="mailto:J.Billington@leeds.ac.uk" class="">J.Billington@leeds.ac.uk</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear experts,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">There is probably a very simple explanation for this glitch but I've been unable to figure it out.<span class="Apple-converted-space"> </span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I've been having a problem with ft_topoplotTRF in which, if I try to only plot a subset of channels, the data is stretched across the whole glass brain (see figure). I've got around this by just plotting
all channels in the past but I'm following the multivariate tutorial and despite using the exact code and data on there I'm still getting the same issue. Is this a bug? Getting it on a couple of recently installed versions of fieldtrip.<span class="Apple-converted-space"> </span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">If I try using the cfg.channel option for the ft_topoplotTRF I get the following error, which I can't understand as ft_channelselection is called fine earlier in the code. </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Undefined function or variable "labelmlo".</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Error in ft_channelselection (line 438)</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">if findmlo,<span class=""> <span class="Apple-converted-space"> </span></span>channel = [channel; labelmlo]; end</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I present the full code below for info.<span class="Apple-converted-space"> </span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you in advance.<span class="Apple-converted-space"> </span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Jac</div>
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<div class="">cfg = [];<br class="">
cfg.output = 'pow';<br class="">
cfg.method = 'mtmconvol';<br class="">
cfg.taper = 'hanning';<br class="">
cfg.foi = 8:2:14;<br class="">
cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5;<br class="">
cfg.channel =<span class="">{'MLO' 'MRO'}</span>;<br class="">
cfg.toi = 2.0:0.1:2.5;<br class="">
cfg.keeptrials = 'yes'; % classifiers operate on individual trials<br class="">
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tfrleft = ft_freqanalysis(cfg, left);<br class="">
tfrright = ft_freqanalysis(cfg, right);<br class="">
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cfg = [];<br class="">
cfg.layout = 'CTF275.lay';<br class="">
cfg.method = 'crossvalidate';<br class="">
cfg.design = [ones(size(tfrleft.powspctrm,1),1); 2*ones(size(tfrright.powspctrm,1),1)]';<br class="">
stat = ft_freqstatistics(cfg,tfrleft,tfrright);<br class="">
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stat.statistic<br class="">
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stat.mymodel = stat.model{1}.primal;<br class="">
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cfg = [];<br class="">
cfg.layout = 'CTF275.lay';<br class="">
cfg.parameter = 'mymodel';<br class="">
cfg.comment = '';<br class="">
%cfg.channel = {'MLO' 'MRO'};<br class="">
cfg.colorbar = 'yes';<br class="">
cfg.interplimits = 'electrodes';<br class="">
ft_topoplotTFR(cfg, stat);<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class="">Dr Jac Billington</span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class="">Lecturer in Cognitive Neuroscience</span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class="">School of Psychology, Rm G.06A</span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class="">University of Leeds</span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class="">Leeds, LS2 9JT</span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class="">Tel: +44(0)113 343 6686</span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class=""> </span></i><i style="" class=""><span style="color: rgb(127, 127, 127);" class=""> </span></i></div>
</i>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class=""><a href="http://medhealth.leeds.ac.uk/profile/1300/983/jac_billington" id="LPNoLP" class="">Jac Billington</a></span></i></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><i class=""><span style="color: rgb(127, 127, 127);" class=""><a href="http://www.leeds.ac.uk/coni/index.html" id="LPNoLP" class="">CoNi Lab</a></span></i></div>
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<span id="cid:CF1C37EB-45FD-45A6-A07D-390338378581@dccn.nl"><topoplotTRF.jpg></span><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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