[FieldTrip] Small presentation error (topoplotTFR)

[Schoffelen, J.M. (Jan Mathijs)]

Dear Jac,

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.
Can you confirm that you don’t have this problem if instead of cfg.layout = ‘CTF275.lay’, you use ‘CTF275_helmet.mat’?

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.

Thanks,
Jan-Mathijs

J.M.Schoffelen, MD PhD
Associate PI, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



On 14 Mar 2019, at 10:37, Jac Billington <J.Billington at leeds.ac.uk<mailto:J.Billington at leeds.ac.uk>> wrote:

Dear experts,

There is probably a very simple explanation for this glitch but I've been unable to figure it out.

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.

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.


Undefined function or variable "labelmlo".
Error in ft_channelselection (line 438)
if findmlo,        channel = [channel; labelmlo]; end

I present the full code below for info.

Thank you in advance.

Jac


cfg              = [];
cfg.output       = 'pow';
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 8:2:14;
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;
cfg.channel      ={'MLO' 'MRO'};
cfg.toi          = 2.0:0.1:2.5;
cfg.keeptrials   = 'yes'; % classifiers operate on individual trials

tfrleft          = ft_freqanalysis(cfg, left);
tfrright         = ft_freqanalysis(cfg, right);

cfg         = [];
cfg.layout  = 'CTF275.lay';
cfg.method  = 'crossvalidate';
cfg.design  = [ones(size(tfrleft.powspctrm,1),1); 2*ones(size(tfrright.powspctrm,1),1)]';
stat        = ft_freqstatistics(cfg,tfrleft,tfrright);

stat.statistic

stat.mymodel = stat.model{1}.primal;

cfg              = [];
cfg.layout       = 'CTF275.lay';
cfg.parameter    = 'mymodel';
cfg.comment      = '';
%cfg.channel      = {'MLO' 'MRO'};
cfg.colorbar     = 'yes';
cfg.interplimits = 'electrodes';
ft_topoplotTFR(cfg, stat);





Dr Jac Billington
Lecturer in Cognitive Neuroscience
School of Psychology, Rm G.06A
University of Leeds
Leeds, LS2 9JT
Tel: +44(0)113 343 6686


Jac Billington<http://medhealth.leeds.ac.uk/profile/1300/983/jac_billington>
CoNi Lab<http://www.leeds.ac.uk/coni/index.html>

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