[FieldTrip] fieldtrip Digest, Vol 41, Issue 34

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Tue Apr 29 15:28:04 CEST 2014


whops, an important correction, I meant Maris, Schoffelen & Fries 2007, 
my bad

On 4/29/2014 11:32 AM, "Jörn M. Horschig" wrote:
> 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>
>>     > -------------- next part --------------
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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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>>     ------------------------------
>>
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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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