[FieldTrip] Coherence of single trials

Tue Nov 27 12:49:38 CET 2012

Dear Monika,

It may have escaped your attention while digging to the previous posts, but the question has been raised (and answered ;-) ) before. Just for the very very last time I will make the following statement:

Single trial coherence estimates cannot be computed!

Perhaps the font size and color will make it memorable ;-). This is due to the simple fact that coherence is defined across observations. If you have just a single observation, due to the mathematics involved, the coherence value will be 1.
Since you want to do group analysis, I think you really should compute the coherence per condition, where each condition should consist of a sufficient number of trials. Assuming that the time domain data is organised such that you have all trials (irrespective of the condition) in a single structure, do something like this.

for each subject
  cfg = [];
  cfg.output = 'fourier';
  cfg.method = 'mtmfft'/'mtmconvol'
  cfg.keeptrials = 'yes';
  ...
  freq = ft_freqanalysis(cfg, data);

  cfg = [];
  cfg.channelcmb = {something here}
  cfg.trials = [indices of trials belonging to condition 1];
  coh1 = ft_connectivityanalysis(cfg, freq); % compute coherence across the trials for condition 1
  cfg.trials = [indices of trials belonging to condition 2];
  coh2 = ft_connectivityanalysis(cfg, freq); % compute coherence across the trials for condition 2
end

Good luck,

Jan-Mathijs

On Nov 27, 2012, at 12:25 PM, Monika Mellem wrote:

> Thank you Sheraz and Jan-Mathijs for your help!  
> Sheraz, if you do have the code to keep single-trial coherence estimates, I would much appreciate it if you could pass it along (monikamellem at gmail.com).  
> And Jan-Mathijs, okay, the necessary statistics make sense, and I will z-transform the data too.  But as far as you know, is there no implementation already in Fieldtrip to keep the single-trial coherence estimates?  I assumed setting cfg.keeptrials = 'yes' would do this, but is there something else I'm missing as this doesn't seem to work?  I would prefer to try what Fieldtrip has implemented first before integrating Sheraz's code into my version of Fieldtrip.
> 
> Thank you very much!
> Monika
> 
> 
> On Tue, Nov 27, 2012 at 3:14 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> wrote:
> 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
> 
> Best,
> 
> Jan-Mathijs
> 
> 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 ');']);
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 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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> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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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