[FieldTrip] fieldtrip Digest, Vol 41, Issue 34
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Tue Apr 29 11:32:35 CEST 2014
Hi Guofa,
What you copied looks to me like squared coherence, whereas FieldTrip
computes absolute coherence. In essence, there is not much difference
(as you can probably infer from the name). In my opinion, it depends
mostly on what statistics you are using and what other methods to find
out what makes most sense. Most papers that I know report coherence, so
I personally prefer coherence because I know what values do make sense.
But that's a matter of choice.
You can check Maris, Schoffelen & Oostenveld, 2007 in JNM for formula
that Fieldtrip uses (see also
http://fieldtrip.fcdonders.nl/references_to_implemented_methods)
Best,
Jörn
On 4/29/2014 4:15 AM, guofa shou wrote:
> 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.):
> Inline image 2
> Inline image 1
> Thanks,
>
>
>
> On Sat, Apr 26, 2014 at 5:00 AM, <fieldtrip-request at science.ru.nl
> <mailto:fieldtrip-request at science.ru.nl>> wrote:
>
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> Today's Topics:
>
> 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
> <mailto:haiteng.jiang at gmail.com>>
> To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] between subject permutation test (guofa shou)
> Message-ID:
>
> <CAHSK_TSjzaqnXgmyKuZXx2w4n8Or7=ESHa93x8hXXP2LaqRGrA at mail.gmail.com <mailto: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 <mailto:guofashou at gmail.com>>
> > To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> > Subject: [FieldTrip] between subject permutation test
> > Message-ID:
> > <
> >
> CAC4CbVLP176SnaPyBDfwqOkdO-jqQnMNFHRTytaQjk5Hsiuaog at mail.gmail.com
> <mailto: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 <tel: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
> <mailto:aaron.schurger at gmail.com>>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <tel:%2B41%2021%20693%201771>
> > aaron.schurger at epfl.ch <mailto:aaron.schurger at epfl.ch>
> > http://lnco.epfl.ch/
> >
> >
> >
> > ------------------------------
> >
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> > fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > 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 <tel:%2B31%20%280%29243668291>
> Web: https://sites.google.com/site/haitengjiang/
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> End of fieldtrip Digest, Vol 41, Issue 34
> *****************************************
>
>
>
>
> --
> Guofa Shou PhD
> Research associate,
> Computational Neuroimaging and Neuroengineering Laboratory,
> University of Oklahoma
> 3100 Monitor Ave. Suit 280
> phone: 405-443-0133
>
>
> _______________________________________________
> 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:
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