[FieldTrip] Two-way permutation test

[Stephen Politzer-Ahles]

Hello Matthias,

It is possible to do a factorial test in Fieldtrip, you just have to hack
the data a little bit. See this post from Eric Maris:
http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests
(also
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-January/003447.html,
which is an older message recommending the same procedure if I remember
correctly)

Best,
Steve





> Message: 7
> Date: Fri, 28 Aug 2015 11:08:55 -0400
> From: David Groppe <david.m.groppe at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Two-way permutation test
> Message-ID:
>         <CAOgkko=yGuk2EX2UFLoA+Zi9bVnMBeNWGt=
> B32PZbahoLy+T0w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Matthias,
>    If I understand you correctly, you can use a t-score based permutation
> test to solve your problem. This procedure can test for an effect of factor
> A, factor B, and their interaction as described here:
>
>
> http://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox:_within-subject_t-tests
>
>    cheers,
>        -David
>
>
> On Fri, Aug 28, 2015 at 9:31 AM, Fritsche, M. (Matthias) <
> m.fritsche at student.ru.nl> wrote:
>
> > Dear Fieldtrip mailing list,
> >
> > my name is Matthias Fritsche and I'm a research intern in Floris de
> > Lange's 'Prediction & Attention' group at the Donders Center for
> Cognitive
> > Neuroimaging. I'm currently working on my Master's project and have got a
> > question I hope you might be able to help me with.
> >
> > I'm currently at the data analysis stage of a behavioral experiment and
> > wondered whether there is a possibility to conduct a two-way permutation
> > test (ANOVA-style, but without actually using ANOVAs/F-values).
> >
> > My experiment has two independent variables, let?s call them A and B, and
> > one dependent variable. Every participant was tested in all of the four
> > conditions, A1B1, A2B1, A1B2 and A2B2. The dependent variable is a
> > parameter of a model that is fit to the data. However, due to unstable
> > fitting at the subject level, I can only obtain this parameter from the
> > group-averaged data.
> >
> > When only interested in effects between two specific conditions, e.g.
> A1B1
> > vs A2B1, the test is straightforward. In order to create the null
> > distribution, I randomly swap the condition labels, A1B1 and A2B1, for
> each
> > participant and compute the resulting group test statistic (difference of
> > the dependent variable between A1B1 and A2B1) for that permutation. One
> > option would be to test the difference between every two conditions in
> this
> > way.
> >
> > However, I wondered whether there is also a way to use a permutation test
> > similar to a 2-way ANOVA, i.e. testing the main effects of factor A and
> > factor B, as well as the interaction effect. For that purpose, there seem
> > to be permutation tests that use ANOVAs to generate permutation
> > distributions of F-values. However, I cannot use ANOVAs since I only have
> > the dependent variable for the whole group and not for individual
> > participants. Do you know of any method to solve this?
> >
> > Thanks for your help.
> >
> > Best,
> > Matthias
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
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