[FieldTrip] Cluster statistics

[Stephen Politzer-Ahles]

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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