[FieldTrip] Coherence of single trials

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Tue Nov 27 09:14:34 CET 2012

Hi Monika,

If you want to test across subjects in  a paired fashion, you can use depsamplesT. Your dependent variable then should contain for each subject and condition the coherence (which of course should be estimated across all trials belonging to that condition). Even better would be to perform a so-called Z-transformation to the data. For some inspiration you could have a look at the following paper: http://www.jneurosci.org/content/31/18/6750.long



On Nov 27, 2012, at 12:22 AM, Monika Mellem wrote:

> Dear Fieldtrippers,
> I am trying to calculate coherence estimates on individual trials of our EEG data and then want to perform a within-subjects statistical test, but so far I have not been able to figure out how to do this.  I am able to calculate coherence for our 22 subjects and then perform statistics on the grand average, so I understand the basic usage of these functions (ft_freqanalysis, ft_connectivityanalysis, ft_freqgrandaverage, ft_freqstatistics).  But now we want to do statistical testing on individual subjects.  Is it possible to keep coherence for individual trials in Fieldtrip as they seem necessary for this statistical analysis?
> I am setting cfg.keeptrials = 'yes' as an input to ft_freqanalysis, and get the cross-spectra of individual trials (I also tried computing the fourier spectra but it made no difference in the following step).  However, when computing the coherence in ft_connectivityanalysis, Fieldtrip averages over the trials.  Is there a way to output coherence for individual trials instead?  Please see the full cfg structure settings below.
> Also, I did look into the option of cfg.statistic = 'indepsamplesZcoh' as an input to ft_freqstatistics since previous posts suggested this was for single subject coherence statistics, but our data is paired as the same stimulus appears in the 2 conditions we are comparing.  Is there a paired test for single subject coherence testing, or should we use cfg.statistic = 'depsamplesT'?
> Many thanks for any suggestions you may have!
> Monika
> ________________
> Monika Mellem
> PhD Candidate
> Interdisciplinary Program in Neuroscience
> Georgetown University
> Washington, DC
> msm79 at georgetown.edu
> 202-687-2687 
> ***********************************************************************
> cfg settings for ft_freqanalysis and ft_connectivityanalysis
> ***********************************************************************
> cfg = [];
> cfg.prestim = -0.5;  
> cfg.poststim = 1.5;  
> cfg.foilim = [2 30];
> cfg.freqrange = 'low';
> % cfg.output     = 'fourier';
> cfg.output     = 'powandcsd';
> cfg.method = 'mtmconvol';
> cfg.keeptrials = 'yes';  
> cfg.channel    = {'all'};  
> cfg.channelcmb = {refchan 'all'}; 
> cfgcoh=[];
> cfgcoh.channelcmb = cfg.channelcmb;
> cfgcoh.method = 'coh';
> v = genvarname(['CRSP_' condition '_low']);
> eval([v '= ft_multitaper_powcoh_EGI(cfg, data);']);  %Wrapper around ft_freqanalysis 
> w = genvarname(['COH_' condition '_low']);
> eval([w '= ft_connectivityanalysis(cfgcoh, ' v ');']);
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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

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