[FieldTrip] Cluster statistics

Tue Nov 13 09:27:04 CET 2012

Dear Caroline,

that's what the option cfg.correcttail = 'alpha'; is for.

Good Luck

Am 13.11.2012 um 09:02 schrieb Lustenberger Caroline:

> Dear Stephen
>  
> Thank you, It now perfectly works, but I always get this warning I'm not sure how to handle that:
>  
> Warning: doing a two-sided test without correcting p-values or alpha-level,
> p-values and alpha-level will reflect one-sided tests per tail
>  
> cfg.clusteralpha = 0.05;
> 
> cfg.alpha = 0.05;
> 
> cfg.clustertail = 0;
> 
> When I want to test whether my data is significant different (direction not known, therefore two sided) with an alpha level <0.05 do I have to adjust my level to 0.025?
>  
> All the Best, Caroline
> 
> Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Stephen Whitmarsh
> Gesendet: Montag, 12. November 2012 17:08
> An: FieldTrip discussion list
> Betreff: Re: [FieldTrip] Cluster statistics
> 
> Dear Caroline,
> 
> Just to be sure - are you working on a recent version of FieldTrip (your pathname suggests otherwise)? The error seems to suggest you are just missing the mexfile which updating your version might solve.
> 
> You can take a look at the specific statfun_* functions for details about their output. A very generic overview is giving in the Fieldtrup Walkthrough (see the left dropdown documentation menu on the website) in which the output input-output structure is explained. That might help as well.
> 
> Cheers,
> Stephen 
> 
> 
> 
> On 12 November 2012 16:55, Lustenberger Caroline <Caroline.Lustenberger at kispi.uzh.ch> wrote:
> Dear Steve
>  
> It seems to work now. However, when I have NaN values in my powerspectrum array, I recieve the following error:
>  
> ??? Invalid MEX-file
> 'C:\Users\Caroline\MATLAB_PhD\fieldtrip-20110927\fieldtrip-20110927\statfun\private\nanmean.mexw64':
> The specified module could not be found.
>  
> Error in ==> statfun_depsamplesT at 98
>     avgdiff = nanmean(diffmat,2);
>  
> Error in ==> statistics_montecarlo at 240
>   [statobs, cfg] = statfun(cfg, dat, design);
>  
> Error in ==> ft_freqstatistics at 279
>   [stat, cfg] = statmethod(cfg, dat, cfg.design);
>  
> What might be the problem?
>  
> Is there a detailed documentation about the command ft_freqstatistics, especially about the meanings of the stats output and what kind of input is possible (e.g. t-test, ...)
>  
> Thanks again for all your help and best wishes
> Caroline
>  
> 
> Von: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] Im Auftrag von Stephen Politzer-Ahles
> Gesendet: Montag, 12. November 2012 14:30
> An: fieldtrip at science.ru.nl
> Betreff: Re: [FieldTrip] Cluster statistics
> 
> Hi Caroline,
> 
> It looks to me like your grand averages don't have any EEG data in them; here is what mine look like:
> 
>          label: {60x1 cell}
>           time: [1x601 double]
>     individual: [19x60x601 double]
>         dimord: 'subj_chan_time'
>            cfg: [1x1 struct]
>           elec: [1x1 struct]
> 
> To run cluster statistics your structure has to have that "individual" field, which has the ERPs for each subject (for instance, from mine you can see I had 19 subjects with a 60-channel cap, and 601 samples in the epoch). I got mine by importing each subject's data into FieldTrip, and then using ft_timelockgrandaverage() with cfg.keepindividual='yes'.
> 
> That is my guess about what your problem is, but I could be wrong. After you ran it, did you check stat.posclusters and stat.negclusters? I think those are more important than stat.stat and stat.prob; they tell you which clusters are actually significant (and stat.posclusterslabelmat and stat.negclusterslabelmat tell you where/when the clusters are).
> 
> Best,
> Steve
> 
> 
> Message: 1
> Date: Sun, 11 Nov 2012 13:25:31 +0000
> From: Lustenberger Caroline <Caroline.Lustenberger at kispi.uzh.ch>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Cluster statistics
> Message-ID: <2B94F80C-7331-45B9-86BF-2ED1123B680A at kispi.uzh.ch>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear fieldtrip users
> 
> I tried to perform cluster analysis with fieldtrip. Since I've performed preprocessing/frequency analysis before using fieldtrip, I had to form the specific
> data structure to use for ft_freqstatistics by myself.
> 
> I made a a structur as follows:
> Condition 1 'EEGa':
> --> 10 subjects:
> EEGa{1:10}
>         label: {128x1 cell} %128 egi elec.
>         dimord: 'chan_freq'
>          freq: 1
>     powspctrm: [128x1 double]
>     cumtapcnt: 1
>           cfg: [1x1 struct]
> 
> Condition 2 'EEGm':
> EEGm{1:10}
>         label: {128x1 cell}
>         dimord: 'chan_freq'
>          freq: 1
>     powspctrm: [128x1 double]
>     cumtapcnt: 1
>           cfg: [1x1 struct]
> 
> 
> Then I performed the following steps:
> 
> cfg = [];
> 
> cfg.elec = elec; %was defined before EGI 128 electrodes
> 
> cfg.neighbours = neighbours; %also successfully defined before
> 
> cfg.latency = 'all';
> 
> %cfg.frequency = 'all';
> 
> cfg.channel = 'all';%eleselection % see CHANNELSELECTION
> 
> cfg.avgovertime = 'no';
> 
> %cfg.avgoverfreq = 'no';
> 
> cfg.avgoverchan = 'no';
> 
> cfg.statistic = 'depsamplesT';
> 
> cfg.numrandomization = 2^10;
> 
> cfg.correctm = 'cluster';
> 
> cfg.method = 'montecarlo';
> 
> cfg.clusteralpha = 0.05;
> 
> cfg.alpha = 0.05;
> 
> cfg.alpha = 0.05;
> 
> cfg.clustertail = 0;
> 
> cfg.feedback = 'gui';
> 
> cfg.parameter = 'powspctrm';
> 
> cfg.design = [
> 
> 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9<tel:9%2010%201%202%203%204%205%206%207%208%209> 10 % subject number
> 
> 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 ]; % condition number
> 
> cfg.uvar = 1; % "subject" is unit of observation
> 
> cfg.ivar = 2; % "condition" is the independent variable
> 
> stat = ft_freqstatistics(cfg, EEGa{:}, EEGm{:});
> 
> 
> 
> 
> The function ft_freqstatistics runs but the stats results are strange.
> My stats.stat is always -inf
> and stats.prob always 0
> 
> What might be the problem?
> 
> 
> Thanks and all the best
> Caroline
> 
> 
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