[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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>> >
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20140424/5199110d/attachment-0001.html
>> > >
>> >
>> > ------------------------------
>> >
>> > 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/
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > fieldtrip mailing list
>> > 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
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