[FieldTrip] selecting which dimension to average over in ft_singleplotER

[jan-mathijs schoffelen]

Hi Matt,

In general, when dealing with time-frequency data, it is advisable to use ft_singleplotTFR, rather than ft_singleplotER. This will show the data both as a function of time and frequency. Interesting that ft_singleplotER works in the first place. If you want to visualize coherence as a function of frequency (i.e. collapsing across time) you can easily do this 'by hand':

C = mean(fd.cohspctrm,3);
figure;plot(fd.freq, C);

Alternatively, you could use 'mtmfft' as a method for your spectral estimation, which yields frequency domain info without a time dimension. 
Once you have this, you can use ft_singleplotER (now it is ER confusingly) to visualize the data.

Best,
Jan-Mathijs

On Nov 7, 2013, at 8:38 PM, mattmizumi at gmail.com wrote:

> A simple newbie question about ft_singleplotER: given a coherence spectrum, as follows,
> 
> fd =
> 
>     labelcmb: {'vStr1'  'vStr2'}
>       dimord: 'chan_freq_time'
>    cohspctrm: [1x100x101 double]
>         freq: [1x100 double]
>         time: [1x101 double]
>          dof: [1x100 double]
>          cfg: [1x1 struct]
> 
> how can I plot frequency against coherence? The default behavior of ft_singleplotER in this case is to average over frequency:
> 
> cfg = [];
> cfg.parameter        = 'cohspctrm';
> cfg.refchannel       = 'vStr2';
> cfg.channel          = 'vStr1';
> ft_singleplotER(cfg, fd);
> 
> selected 1 channels for cohspctrm
> selection cohspctrm along dimension 2
> averaging cohspctrm over freq
> the call to "ft_singleplotER" took 0 seconds
> 
> ..but I cannot find a way to get it to average over time instead. How can I do this?
> 
> (Of course, I know I can plot this manually. But I would like to understand how to use the ft plotting functions. I can't find anything pertinent in the coherence and plotting tutorials, or the help for ft_singleplotER.)
> 
> Thanks!
> 
> -- Matt
> _______________________________________________
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> fieldtrip at donders.ru.nl
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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