[FieldTrip] Permutation statistics

[Vitoria Piai]

Hi Hweeling,

I'm sorry, I don't understand exactly what you mean by "within-trial" 
analysis.

If you mean comparing trials within the same participant, then there are 
two things you should change in your code:
   cfg.statistic = 'indepsamplesT';  %% this should be indepsamplesT 
rather than depsamplesT
   cfg.uvar = 1; %%% Remove this line from your configuration
     cfg.ivar = 1;  %% the indep. var here should be 1, rather than 2

Maybe your design will also need some adjustment, I'm not so sure (I 
don't use indepsamplesT that much). In any case, it could help to have a 
look at: 
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock?s[]=indepsamplest

If you want a cleaner code, you can also remove all these lines (they 
should be default):
cfg.channel = 'all';
     cfg.latency = 'all';
     cfg.trials = 'all';
     cfg.frequency = 'all';

I hope this works, otherwise email the list again.
Good luck, Vitória



On 3/23/2014 3:19 PM, Hwee Ling Lee wrote:
> Dear Vitoria,
>
> Thanks for the tip.
>
> I'm trying to perform a within-trial analysis.
>
> I've got two sets of data, before and after resting state EEG 
> activity. First set has 54 trials and second set has 51 trials. Hence, 
> my cfg.design = [ones(1, 105); ones(1,54), ones(1,51)*2].
>
> I've set up the statistical analysis like this:
>
>     cfg = [];
>     cfg.layout = lay;
>     cfg.channel = 'all';
>     cfg.latency = 'all';
>     cfg.trials = 'all';
>     cfg.frequency = 'all';
>     cfg.avgovertime = 'no';
>     cfg.avgoverfreq = 'no';
>     cfg.avgoverchan = 'no';
>     cfg.parameter = 'powspctrm';
>     cfg.method = 'montecarlo';
>     cfg.statistic = 'depsamplesT';
>     cfg.numrandomization = 1000;
>     cfg.design = design;
>     cfg.uvar = 1;
>     cfg.ivar = 2;
>     [stat] = ft_freqstatistics(cfg, post_c200freq, pre_c200freq);
>
> However, I got an error message:
>
> Error using ft_statfun_depsamplesT (line 84)
> Invalid specification of the design array.
>
> Error in ft_statistics_montecarlo (line 285)
>   [statobs, cfg] = statfun(cfg, dat, design);
>
> Error in ft_freqstatistics (line 323)
>   [stat, cfg] = statmethod(cfg, dat, cfg.design);
>
> Can someone please tell me what parameters did I specify wrongly? Thanks.
>
> Best wishes,
> Hweeling
>
>
>
>
> On 21 March 2014 20:10, Vitória Piai <v.piai.research at gmail.com 
> <mailto:v.piai.research at gmail.com>> wrote:
>
>     Dear Hweeling,
>
>     There is nothing inherent to the ft_freqstatistics function that
>     makes it special for MEG, rather than for EEG data. If you've been
>     using other FieldTrip functions, you probably have used
>     cfg.channel before. These are the channels present in your EEG data.
>     How you should set some of the other parameters depends only on
>     your design, not on whether the data are from MEG or EEG.
>     Maybe you can specify what is unclear to you when calling the
>     function so that you can get appropriate help!
>
>     Good luck, Vitoria
>
>
>     On 3/21/2014 3:36 PM, Hwee Ling Lee wrote:
>>
>>     Dear all,
>>
>>     I've got EEG datasets for 64 channels, and I would like to
>>     perform permutation statistics on the power frequency analyses to
>>     compare the two conditions (before and after resting state periods).
>>
>>     However, I'm not sure how to operationalise the statistical
>>     analyses since most of the examples on the website are for MEG
>>     datasets.
>>
>>     I would appreciate very much if someone could help me on this!
>>     Thanks!
>>
>>     Cheers,
>>     Hweeling
>>
>>
>>
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl  <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> -- 
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de <http://dzne.de>
> Email 2: hweeling.lee<at>gmail.com <http://gmail.com>
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================

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