[FieldTrip] Problem with clustering across electrode neighbours

["Jörn M. Horschig"]

Hey Duncan,

it looks pretty much like you are using an old FieldTrip version with a 
new neighbourhood-structure. Could you check the with the most recent 
version again?
Some months (about a year?) ago we changed the neighbour definition from 
cell arrays to structure arrays, so any attempt to access 
cfg.neighbours{i} will fail, cause it has to be cfg.neighbours(i) 
instead. But as I already said, this has been changed quite some time 
back in the past :)

Essentially, your code is fine, but some note that cfg.neighbourdist 
should be a scalar, not the string 'number', but only if 
cfg.method='distance'. If you choose cfg.method = 'template' then 
cfg.neighbourdist is not used, cause a template is loaded.

Best,
Jörn

On 9/13/2012 12:46 PM, Duncan Astle wrote:
>
> Dear Fieldtrippers,
>
> I am rather new to this, but am attempting to do some cluster stats on 
> my ERP sensor level data. It is working well, and I can cluster across 
> time, but I can't get it to cluster across electrode locations. I 
> think it is because of a mistake that I am making in my 'neighbours' 
> file, although it looks fine when I inspect it. This is the error 
> message that I get:
>
> ??? Cell contents reference from a non-cell array object.
>
> Error in ==> clusterstat>makechanneighbstructmat at 520
>
>     [seld] = match_str(cfg.channel, cfg.neighbours{chan}.label);
>
> Error in ==> clusterstat at 60
>
>     channeighbstructmat = makechanneighbstructmat(cfg);
>
> Error in ==> statistics_montecarlo at 322
>
>   [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource);
>
> Error in ==> statistics_wrapper at 285
>
>     [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource);
>
> Error in ==> ft_timelockstatistics at 119
>
> [stat, cfg] = statistics_wrapper(cfg, varargin{:});
>
> Can anyone spot what I am doing wrong?
>
> This is how I make my neighbour file:
>
> cfg = [];
>
> cfg.layout      = 'EEG1010.lay'; % try 'distance' as well
>
> cfg.feedback    = 'yes'; % show a neighbour plot
>
> cfg.method      = 'template';
>
> cfg.neighbourdist = 'number';
>
> cfg.template      = 'EEG1010_neighb.mat'
>
> cfg.channel       = 'all'
>
> cfg.feedback      = 'yes';
>
> neighbours      = ft_prepare_neighbours(cfg, Load5Hard); % define 
> neighbouring channels
>
> This is how I then try the stats:
>
>     cfg = [];
>
>     cfg.channel     = 'all';
>
>     cfg.latency     = [0.1 1.3];
>
>     cfg.avgovertime = 'no';
>
>     cfg.avgoverchannel = 'no';
>
>     cfg.parameter   = 'individual';
>
>     cfg.method      = 'montecarlo';
>
>     cfg.statistic   = 'depsamplesT'
>
>     cfg.alpha       = 0.05;
>
>     cfg.correctm    = 'cluster';
>
>     cfg.correcttail = 'prob';
>
>     cfg.numrandomization = 1000;
>
>     cfg.feedback    = 'yes'; % show a neighbour plot
>
>     cfg.neighbours  = neighbours;
>
> %cfg.minnbchan        = 2;
>
>     cfg.clusterstatistic = 'maxsum';
>
>     cfg.clusterthreshold = 'nonparametric';
>
>     cfg.clusteralpha     = 0.01;
>
>     cfg.clustercritval   = 0.06;
>
> % cfg.clustertail      = 0;
>
>     cfg.tail = 0;
>
>     Nsub = 19;
>
>     cfg.design(1,1:2*Nsub)  = [ones(1,Nsub) 2*ones(1,Nsub)];
>
>     cfg.design(2,1:2*Nsub)  = [1:Nsub 1:Nsub];
>
>     cfg.ivar                = 1; % the 1st row in cfg.design contains 
> the independent variable
>
>     cfg.uvar                = 2; % the 2nd row in cfg.design contains 
> the subject number
>
> [stat] = ft_timelockstatistics(cfg, Load3Hard, Load3Easy)
>
> Any suggestions very gratefully received.
>
> Thanks,
>
> Duncan
>
> ________________________________________________
>
> Dr. Duncan Astle,
>
> Programme Leader Track,
>
> British Academy Research Fellow,
>
> MRC Cognition and Brain Sciences Unit,
>
> Chaucer Road,
>
> Cambridge.
>
> Duncan.Astle at mrc-cbu.cam.ac.uk
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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