[FieldTrip] Cluster statistics

[Stephen Whitmarsh]

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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