options for cluster-based permutation tests

[jan-mathijs schoffelen]

Dear Enrico,

It seems that cfg.neighbourdist should do the trick:

The generation of lists of neighbouring channels for each channel is  
done by the function neighbourselection. As far as I can see, the  
inclusion of neighbours is indeed based on the distance.
Putting it to zeros should be OK. Another way of going about it, is  
to explicitly define the neighbourhood structure in the configuration:

cfg.neighbours = [];
for k = 1:length(choi)
   cfg.neighbours.label{k} = choi{k};
   cfg.neighbours.neighblabel = {};
end

This prevents statistics_wrapper.m to go into the computation of the  
neighbourhood altogether.

Good luck,

Jan-Mathijs

On Jun 26, 2008, at 5:14 PM, Enrico Glerean wrote:

> Hello dear people,
>
> I have a very quick question that hopefully has not been answered  
> before:
> we have to run cluster based permutation tests using clustering in  
> time
> and frequency but not in space. Which means not considering neighbor
> channels.
>
> I think that the best option would be using the parameter
>
> cfg.neighbourdist    = 0.0;
>
> which means that there are no neighbor electrodes.
>
> Is that correct or is there a better option? Should cfg.minnbchan be
> changed as well and set to 0?
>
>
> the whole lists of config parameters passed to freqstatistics()  
> would be:
>
> cfg = [];
> cfg.channel = choi;
> cfg.method = 'montecarlo';
> cfg.statistic = 'depsamplesT';
> cfg.tail = 0;
> cfg.alpha = 0.05;
> cfg.numrandomization = 5;
>
> cfg.correctm='cluster';
> cfg.clusteralpha = 0.05;
> cfg.clusterstatistic = 'maxsum';
> cfg.minnbchan = 0;
> cfg.clustertail = 0;
> cfg.neighbourdist    = 0.0;
>
>
> thanks in advance for your help
>
> best regards
>
> -- 
> Enrico Glerean
> englerea at cc.jyu.fi
> Jyväskylä, Finland
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.