[FieldTrip] fieldtrip Digest, Vol 41, Issue 34
guofa shou
guofashou at gmail.com
Tue Apr 29 04:15:15 CEST 2014
Thanks, Haiteng.
And I have one more question about which coherence equation was used in
Fieldtrip? I have checked the code, it seems it is different compared to
the following equation (from Srinivasan, Ramesh, et al. "EEG and MEG
coherence: measures of functional connectivity at distinct spatial scales
of neocortical dynamics." *Journal of neuroscience methods* 166.1 (2007):
41-52.):
[image: Inline image 2]
[image: Inline image 1]
Thanks,
On Sat, Apr 26, 2014 at 5:00 AM, <fieldtrip-request at science.ru.nl> wrote:
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> 1. Re: between subject permutation test (guofa shou) (Haiteng Jiang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 25 Apr 2014 13:35:40 +0200
> From: Haiteng Jiang <haiteng.jiang at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] between subject permutation test (guofa shou)
> Message-ID:
> <CAHSK_TSjzaqnXgmyKuZXx2w4n8Or7=
> ESHa93x8hXXP2LaqRGrA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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=
> > 8HFQpK3HHf6-Ba0g at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > 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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> End of fieldtrip Digest, Vol 41, Issue 34
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>
--
Guofa Shou PhD
Research associate,
Computational Neuroimaging and Neuroengineering Laboratory,
University of Oklahoma
3100 Monitor Ave. Suit 280
phone: 405-443-0133
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