[FieldTrip] between subject permutation test (guofa shou)

[Haiteng Jiang]

Hi Guofa,
     This is quite similar to between trial experiment (
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq). In your
case, you could specify something like this:

cfg.statistic        = 'indepsamplesT';
design               = zeros(1,22);
design(1,10)          = 1;  % group 1
design(1,11:22)      = 2;   % group 2
cfg.design           = design;
cfg.ivar              = 1;

                 Best,

                 Haiteng



>
> Message: 2
> Date: Thu, 24 Apr 2014 09:54:10 -0500
> From: guofa shou <guofashou at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] between subject permutation test
> Message-ID:
>         <
> CAC4CbVLP176SnaPyBDfwqOkdO-jqQnMNFHRTytaQjk5Hsiuaog at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi, Fieldtripers,
>    I have a question about the parameters setting about running
> cluster-based permutation test on group-level frequency data. Specifically,
> I have two groups, one is 12 subjects (i.e., 12 averaged powers), the other
> is 10 subjects (10 averaged powers), I want to do comparison on the sensor
> powers between these two groups. so how can I set cfg.statistic,
> cfg.design.
>    Thanks!
> Guofa
>
> --
> Guofa Shou PhD
> Research fellow,
> Computational Neuroimaging and Neuroengineering Laboratory,
> University of Oklahoma
> 3100 Monitor Ave. Suit 280
> phone: 405-496-8661
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> Message: 3
> Date: Thu, 24 Apr 2014 18:24:44 +0200
> From: Aaron Schurger <aaron.schurger at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] cluster based permutation test -
>         cfg.clusteralpha        threshold
> Message-ID:
>         <CALeeyATd6KopUY=NTuHsPwNST5kdK=-Wq=
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>
> Dear Balint,
> It was difficult to parse your question: "it?s a valid way to choose a
> more permissive threshold (cfg.clusteralpha) at the level of the
> clusters identifying t-tests?" If you are asking whether or not it is
> valid to use a lower point-wise threshold, then it is technically
> valid, but if, for example, you try every possible point-wise
> threshold from 0.01 to 0.20 in steps of 0.01, and you manage to find
> one that gives you a significant result - well that should be avoided.
> Otherwise it is OK. You might also try this:
> http://www.biomedcentral.com/1471-2202/14/122 with code available
> here: https://bitbucket.org/emsf/emsf_matlab
>
> Instead of trying to find clusters of points that covary with an
> experimental effect, you try to find a temporo-spatial weighting that
> maximizes the experimental effect, and then look at the spatial
> patterns (clusters) that give you the effect.
>
> Best,
> Aaron
>
> On Thu, Apr 24, 2014 at 4:23 PM, Balint File <file.balint at ttk.mta.hu>
> wrote:
> > Dear Fieldtrip experts,
> >
> > Recently I started to apply the spatial dimension (electrode
> neighborhood)
> > of the cluster based permutation test. My question is: it?s a valid way
> to
> > choose a more permissive threshold (cfg.clusteralpha) at the level of the
> > clusters identifying t-tests? According to the publication of Maris et
> al.,
> > 2007 (?this threshold does not affect the FA rate of the statistical
> test.
> > However, this threshold does affect the sensitivity of the test. For
> > example, weak but long-lasting effects are not detected when the
> threshold
> > is large?) it seems to me, that this threshold depends on the nature of
> the
> > data. For lower cfg.clusteralpha  threshold (<0.15) I get more extensive
> > (and more explainable)  results and the clusters still show high
> > significance (<<0.025) at the permutation test.
> >
> > Thanks in advance for your help.
> >
> > Best regards,
> >
> > B?lint File
> >
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Aaron Schurger, PhD
> Senior researcher
> Laboratory of Cognitive Neuroscience
> Brain-Mind Institute, Department of Life Sciences
> ?cole Polytechnique F?d?rale de Lausanne
> Station 19, AI 2101
> 1015 Lausanne, Switzerland
> +41 21 693 1771
> aaron.schurger at epfl.ch
> http://lnco.epfl.ch/
>
>
>
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> End of fieldtrip Digest, Vol 41, Issue 33
> *****************************************
>



-- 
Haiteng Jiang
PhD candidate
Neuronal Oscillations Group
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen

Visiting address
Room 2.32
Donders Centre for Cognitive Neuroimaging
Kapittelweg 29
6525 EN  Nijmegen
the Netherlands

 Tel.: +31 (0)243668291
 Web:  https://sites.google.com/site/haitengjiang/
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