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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks very much for the responses Stephan and J</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">örn!
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">One last question if possible Jörn. In your opinion, will doing several (at the most 5) cluster based t-tests affect the validity of permutation
method testing to control for multiple comparisons? Would being more conservative regarding my alpha (for example a combination of permutation AND Bonferroni) possibly alleviate this?
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><br>
Thanks again for the responses, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Peter.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> fieldtrip-bounces@science.ru.nl
[mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>"Jörn M. Horschig"<br>
<b>Sent:</b> Monday, 24 September 2012 10:15 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Neuromag sensor level stats<o:p></o:p></span></p>
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<p class="MsoNormal">Dear Peter,<br>
<br>
regarding your first question, most people here at the Donders actually repair bad channels. When computing the grandaverage over subjects or doing some statistics across subjects, only those channels which are in common for all datasets are used. Thus, if
having different channels damaged/rejected per subjects, you can end up with a fairly low amount of channels. But, in the end it depends pretty much on what channels you reject wrt your hypothesis, e.g. having few occipital channels while being interested
in motor regions won't constitute a big problem, so no need to interpolate. I leave the question whether it's a correct thing to do up to you (imho: I wouldn't worry too much about it).<br>
<br>
Regarding your third question: In FieldTrip you can only compare two conditions directly (at least when doing cluster-based permutation testing). Also, any interaction needs to be setup manually.<br>
<br>
Best,<br>
Jörn<br>
<br>
On 9/23/2012 3:14 PM, Peter Goodin wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Hi Fieldtrippers,
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">I'm at a stage where I'd like to do statistical analysis on my ERF neuromag data, but don't really know where to begin. I'd like to do a cluster analysis, but the tutorial
material is for a CTF system. I'm using a neuromag 306 channel which complicates matters somewhat due to the different sensor types. I've searched the mailing list but can't find any solid answers / example scripts. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">The most pressing questions I have are: <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">1. Despite running the data through maxfilter and entering in the bad channels, occasionally one gets through (not the same one). I've used Fieldtrip's repairchannel function
on the data, making sure to replace the channel only with like sensor neighbouring sensors. While I know this is a common method for fixing bad channels in EEG, does the same hold for MEG due to non-existent smearing of the signal? Is it best to keep the fixed
channel(s) or just remove them from the stats analysis across all participants? <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">2. Given the three sensor types on the neuromag system, do I need to run three different cluster analyses (one for mags, one for xgrads, one for ygrads), each time specifying
like sensor neighbours? Alternatively, If I'm not interested in the mags data, can I just run one using the data from the combined gradiometers?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">3. When examining for group x condition effects, would I use a three row design matrix with row 1 containing group, row 2 containing participants and row 3 conditions?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Thanks for any help, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Peter<o:p></o:p></span></p>
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<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>fieldtrip mailing list<o:p></o:p></pre>
<pre><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><o:p></o:p></pre>
<pre><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Jörn M. Horschig<o:p></o:p></pre>
<pre>PhD Student<o:p></o:p></pre>
<pre>Donders Institute for Brain, Cognition and Behaviour <o:p></o:p></pre>
<pre>Centre for Cognitive Neuroimaging<o:p></o:p></pre>
<pre>Radboud University Nijmegen <o:p></o:p></pre>
<pre>Neuronal Oscillations Group<o:p></o:p></pre>
<pre>FieldTrip Development Team<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>P.O. Box 9101<o:p></o:p></pre>
<pre>NL-6500 HB Nijmegen<o:p></o:p></pre>
<pre>The Netherlands<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Contact:<o:p></o:p></pre>
<pre>E-Mail: <a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><o:p></o:p></pre>
<pre>Tel: +31-(0)24-36-68493<o:p></o:p></pre>
<pre>Web: <a href="http://www.ru.nl/donders">http://www.ru.nl/donders</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Visiting address:<o:p></o:p></pre>
<pre>Trigon, room 2.30<o:p></o:p></pre>
<pre>Kapittelweg 29<o:p></o:p></pre>
<pre>NL-6525 EN Nijmegen<o:p></o:p></pre>
<pre>The Netherlands<o:p></o:p></pre>
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