[FieldTrip] Coherence of single trials

[Monika Mellem]

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
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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