<div dir="ltr">Thanks, <span style="font-family:arial,sans-serif;font-size:13px"> Haiteng.</span><div><font face="arial, sans-serif">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 </font><span style="font-size:13px;font-family:Arial,sans-serif;line-height:16.1200008392334px">Srinivasan, Ramesh, et al. "EEG and MEG coherence: measures of functional connectivity at distinct spatial scales of neocortical dynamics." </span><i style="font-size:13px;font-family:Arial,sans-serif;line-height:16.1200008392334px">Journal of neuroscience methods</i><span style="font-size:13px;font-family:Arial,sans-serif;line-height:16.1200008392334px"> 166.1 (2007): 41-52.</span><span style="font-family:arial,sans-serif">):</span></div>
<div><font face="arial, sans-serif"><img src="cid:ii_145ab43028edb9e3" alt="Inline image 2" width="337" height="57"><br></font></div><div><font face="arial, sans-serif"><img src="cid:ii_145ab42cf4db84cb" alt="Inline image 1" width="184" height="57"><br>
</font></div><div><font face="arial, sans-serif">Thanks,</font></div><div><font face="arial, sans-serif"><br></font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Apr 26, 2014 at 5:00 AM, <span dir="ltr"><<a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a>></span> wrote:<br>
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Today's Topics:<br>
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1. Re: between subject permutation test (guofa shou) (Haiteng Jiang)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 25 Apr 2014 13:35:40 +0200<br>
From: Haiteng Jiang <<a href="mailto:haiteng.jiang@gmail.com">haiteng.jiang@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: Re: [FieldTrip] between subject permutation test (guofa shou)<br>
Message-ID:<br>
<CAHSK_TSjzaqnXgmyKuZXx2w4n8Or7=<a href="mailto:ESHa93x8hXXP2LaqRGrA@mail.gmail.com">ESHa93x8hXXP2LaqRGrA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Guofa,<br>
This is quite similar to between trial experiment (<br>
<a href="http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq</a>). In your<br>
case, you could specify something like this:<br>
<br>
cfg.statistic = 'indepsamplesT';<br>
design = zeros(1,22);<br>
design(1,10) = 1; % group 1<br>
design(1,11:22) = 2; % group 2<br>
cfg.design = design;<br>
cfg.ivar = 1;<br>
<br>
Best,<br>
<br>
Haiteng<br>
<br>
<br>
<br>
><br>
> Message: 2<br>
> Date: Thu, 24 Apr 2014 09:54:10 -0500<br>
> From: guofa shou <<a href="mailto:guofashou@gmail.com">guofashou@gmail.com</a>><br>
> To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
> Subject: [FieldTrip] between subject permutation test<br>
> Message-ID:<br>
> <<br>
> <a href="mailto:CAC4CbVLP176SnaPyBDfwqOkdO-jqQnMNFHRTytaQjk5Hsiuaog@mail.gmail.com">CAC4CbVLP176SnaPyBDfwqOkdO-jqQnMNFHRTytaQjk5Hsiuaog@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi, Fieldtripers,<br>
> I have a question about the parameters setting about running<br>
> cluster-based permutation test on group-level frequency data. Specifically,<br>
> I have two groups, one is 12 subjects (i.e., 12 averaged powers), the other<br>
> is 10 subjects (10 averaged powers), I want to do comparison on the sensor<br>
> powers between these two groups. so how can I set cfg.statistic,<br>
> cfg.design.<br>
> Thanks!<br>
> Guofa<br>
><br>
> --<br>
> Guofa Shou PhD<br>
> Research fellow,<br>
> Computational Neuroimaging and Neuroengineering Laboratory,<br>
> University of Oklahoma<br>
> 3100 Monitor Ave. Suit 280<br>
> phone: <a href="tel:405-496-8661" value="+14054968661">405-496-8661</a><br>
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> ------------------------------<br>
><br>
> Message: 3<br>
> Date: Thu, 24 Apr 2014 18:24:44 +0200<br>
> From: Aaron Schurger <<a href="mailto:aaron.schurger@gmail.com">aaron.schurger@gmail.com</a>><br>
> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Subject: Re: [FieldTrip] cluster based permutation test -<br>
> cfg.clusteralpha threshold<br>
> Message-ID:<br>
> <CALeeyATd6KopUY=NTuHsPwNST5kdK=-Wq=<br>
> <a href="mailto:8HFQpK3HHf6-Ba0g@mail.gmail.com">8HFQpK3HHf6-Ba0g@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset=UTF-8<br>
><br>
> Dear Balint,<br>
> It was difficult to parse your question: "it?s a valid way to choose a<br>
> more permissive threshold (cfg.clusteralpha) at the level of the<br>
> clusters identifying t-tests?" If you are asking whether or not it is<br>
> valid to use a lower point-wise threshold, then it is technically<br>
> valid, but if, for example, you try every possible point-wise<br>
> threshold from 0.01 to 0.20 in steps of 0.01, and you manage to find<br>
> one that gives you a significant result - well that should be avoided.<br>
> Otherwise it is OK. You might also try this:<br>
> <a href="http://www.biomedcentral.com/1471-2202/14/122" target="_blank">http://www.biomedcentral.com/1471-2202/14/122</a> with code available<br>
> here: <a href="https://bitbucket.org/emsf/emsf_matlab" target="_blank">https://bitbucket.org/emsf/emsf_matlab</a><br>
><br>
> Instead of trying to find clusters of points that covary with an<br>
> experimental effect, you try to find a temporo-spatial weighting that<br>
> maximizes the experimental effect, and then look at the spatial<br>
> patterns (clusters) that give you the effect.<br>
><br>
> Best,<br>
> Aaron<br>
><br>
> On Thu, Apr 24, 2014 at 4:23 PM, Balint File <<a href="mailto:file.balint@ttk.mta.hu">file.balint@ttk.mta.hu</a>><br>
> wrote:<br>
> > Dear Fieldtrip experts,<br>
> ><br>
> > Recently I started to apply the spatial dimension (electrode<br>
> neighborhood)<br>
> > of the cluster based permutation test. My question is: it?s a valid way<br>
> to<br>
> > choose a more permissive threshold (cfg.clusteralpha) at the level of the<br>
> > clusters identifying t-tests? According to the publication of Maris et<br>
> al.,<br>
> > 2007 (?this threshold does not affect the FA rate of the statistical<br>
> test.<br>
> > However, this threshold does affect the sensitivity of the test. For<br>
> > example, weak but long-lasting effects are not detected when the<br>
> threshold<br>
> > is large?) it seems to me, that this threshold depends on the nature of<br>
> the<br>
> > data. For lower cfg.clusteralpha threshold (<0.15) I get more extensive<br>
> > (and more explainable) results and the clusters still show high<br>
> > significance (<<0.025) at the permutation test.<br>
> ><br>
> > Thanks in advance for your help.<br>
> ><br>
> > Best regards,<br>
> ><br>
> > B?lint File<br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > fieldtrip mailing list<br>
> > <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> > <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
><br>
><br>
> --<br>
> Aaron Schurger, PhD<br>
> Senior researcher<br>
> Laboratory of Cognitive Neuroscience<br>
> Brain-Mind Institute, Department of Life Sciences<br>
> ?cole Polytechnique F?d?rale de Lausanne<br>
> Station 19, AI 2101<br>
> 1015 Lausanne, Switzerland<br>
> <a href="tel:%2B41%2021%20693%201771" value="+41216931771">+41 21 693 1771</a><br>
> <a href="mailto:aaron.schurger@epfl.ch">aaron.schurger@epfl.ch</a><br>
> <a href="http://lnco.epfl.ch/" target="_blank">http://lnco.epfl.ch/</a><br>
><br>
><br>
><br>
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> End of fieldtrip Digest, Vol 41, Issue 33<br>
> *****************************************<br>
><br>
<br>
<br>
<br>
--<br>
Haiteng Jiang<br>
PhD candidate<br>
Neuronal Oscillations Group<br>
Donders Institute for Brain, Cognition and Behaviour<br>
Centre for Cognitive Neuroimaging<br>
Radboud University Nijmegen<br>
<br>
Visiting address<br>
Room 2.32<br>
Donders Centre for Cognitive Neuroimaging<br>
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6525 EN Nijmegen<br>
the Netherlands<br>
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End of fieldtrip Digest, Vol 41, Issue 34<br>
*****************************************<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family:monospace;font-size:16px">Guofa Shou PhD</span><br style="font-family:monospace;font-size:16px"><span style="font-family:monospace;font-size:16px">Research associate,</span><br style="font-family:monospace;font-size:16px">
<span style="font-family:monospace;font-size:16px">Computational Neuroimaging and Neuroengineering Laboratory,</span><br style="font-family:monospace;font-size:16px"><span style="font-family:monospace;font-size:16px">University of Oklahoma</span><br style="font-family:monospace;font-size:16px">
<span style="font-family:monospace;font-size:16px">3100 Monitor Ave. Suit 280</span><br style="font-family:monospace;font-size:16px"><span style="font-family:monospace;font-size:16px">phone: 405-443-0133</span></div>
</div>