[FieldTrip] Problem with clustering across electrode neighbours
Duncan Astle
Duncan.Astle at mrc-cbu.cam.ac.uk
Fri Sep 14 16:58:26 CEST 2012
Thanks for your help. You were spot on; now the version is updated it runs perfectly.
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
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig"
Sent: 13 September 2012 12:11
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Problem with clustering across electrode neighbours
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<mailto:Duncan.Astle at mrc-cbu.cam.ac.uk>
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--
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<mailto: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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