<div dir="ltr">Hi Guofa,<div> This is quite similar to between trial experiment (<a href="http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq">http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq</a>). In your case, you could specify something like this:</div>
<div><br></div><div><pre class="" style="padding:0.5em;margin-top:0px;border:1px dashed rgb(204,204,204);overflow:hidden;background-color:rgb(247,249,250);width:640px;text-align:justify"><font color="#000000" face="Consolas, Andale Mono, Menlo, Monaco, monospace"><span style="white-space:pre-wrap">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;<br></span></font></pre><pre class="" style="padding:0.5em;margin-top:0px;font-size:12px;border:1px dashed rgb(204,204,204);color:rgb(0,0,0);overflow:hidden;font-family:Consolas,'Andale Mono',Menlo,Monaco,monospace;background-color:rgb(247,249,250);white-space:pre-wrap;width:640px;text-align:justify">
Best,</pre><pre class="" style="padding:0.5em;margin-top:0px;font-size:12px;border:1px dashed rgb(204,204,204);color:rgb(0,0,0);overflow:hidden;font-family:Consolas,'Andale Mono',Menlo,Monaco,monospace;background-color:rgb(247,249,250);white-space:pre-wrap;width:640px;text-align:justify">
Haiteng </pre><div class="gmail_extra"><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<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>
<<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, 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: 405-496-8661<br>
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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=<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>> wrote:<br>
> Dear Fieldtrip experts,<br>
><br>
> Recently I started to apply the spatial dimension (electrode neighborhood)<br>
> of the cluster based permutation test. My question is: it?s a valid way 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 al.,<br>
> 2007 (?this threshold does not affect the FA rate of the statistical 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 threshold<br>
> is large?) it seems to me, that this threshold depends on the nature of 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>
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<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>
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End of fieldtrip Digest, Vol 41, Issue 33<br>
*****************************************<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><div><font face="arial, helvetica, sans-serif">Haiteng Jiang</font></div><div><font face="arial, helvetica, sans-serif">PhD candidate</font></div><div><font face="arial, helvetica, sans-serif">Neuronal Oscillations Group</font></div>
<div><font face="arial, helvetica, sans-serif">Donders Institute for Brain, Cognition and Behaviour</font></div><div><font face="arial, helvetica, sans-serif">Centre for Cognitive Neuroimaging</font></div><div><font face="arial, helvetica, sans-serif">Radboud University Nijmegen</font></div>
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