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<p class=MsoNormal>Hi Eric,<o:p></o:p></p>
<p class=MsoNormal>Thank you very much for the fast response. So if I
understand correctly, for a cluster map with X clusters the largest cluster is
compared to a permutation distribution created from the largest ClusterStat of
each permutation, the 2<sup>nd</sup> largest cluster to a distribution
constructed from the 2<sup>nd</sup> ClusterStat of each, etc. If this is correct
and the largest cluster is just being tested using Max(ClusterStat), why do you
say that this vector-based approach has less power for the largest cluster?
Also, the permutation distribution for the smaller clusters may not have all
1000 values if some permutations have fewer clusters, right? I appreciate
the advice.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Best,<o:p></o:p></p>
<p class=MsoNormal>Allen <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>__________________________________________________________________________________</span><o:p></o:p></p>
<p class=MsoNormal>Allen Ardestani Email: <a
href="mailto:aardesta@ucla.edu"><span style='color:blue'>aardesta@ucla.edu</span></a><o:p></o:p></p>
<p class=MsoNormal>Phone: (310) 825-5528<o:p></o:p></p>
<p class=MsoNormal>Medical Scientist Training Program<o:p></o:p></p>
<p class=MsoNormal>David Geffen School of Medicine at UCLA<o:p></o:p></p>
<p class=MsoNormal>Semel Institute for Neuroscience and Human Behavior<o:p></o:p></p>
<p class=MsoNormal>760 Westwood Plaza<o:p></o:p></p>
<p class=MsoNormal>Los Angeles, CA 90095-1759<o:p></o:p></p>
<p class=MsoNormal>USA<o:p></o:p></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> FieldTrip
discussion list [mailto:FIELDTRIP@NIC.SURFNET.NL] <b>On Behalf Of </b>Eric
Maris<br>
<b>Sent:</b> Thursday, July 01, 2010 2:55 PM<br>
<b>To:</b> FIELDTRIP@NIC.SURFNET.NL<br>
<b>Subject:</b> Re: [FIELDTRIP] Vector-valued ClusterStats<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span lang=NL style='font-family:"Verdana","sans-serif";
color:#1F497D'>Hi Allen,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=NL style='font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=NL style='font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal>I’ve already looked at the 2007 JMN paper by Maris and
Oostenveld, but still have some remaining questions about using a vector-valued
test statistic to assess differences between 2 conditions (correct vs incorrect
memory task performance). I’ve attached a cluster map showing the
many different sizes and shapes that make it necessary to use a vector-valued
test statistic.<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>The
different sizes and shapes of the clusters does not force one to use a
vector-valued test statistic.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Do the existing FT functions handle vector-valued
stats?<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Vector-valued
stats are not supported by the ft_timelockstatistics and ft_freqstatistics
functions (which call statistics_montecarlo). They are supported by the older
function clusterrandanalysis, but I’m not sure how this function will
behave give that Fieldtrip has gone through several changes.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Don’t
expect too much of a vector-valued test statistic. For detecting the largest
cluster, the vector-valued test statistic has LESS power than the scalar test
statistic (Max(clusterstat)). I have played around with the vector-valued test
statistic but there were few cases where it made a difference.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Are all ClusterStats from each permutation (bigger than
a minimum size) included when constructing a multivariate permutation
distribution?<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Yes.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Are clusters of all sizes compared to the same
permutation distribution? I.e., would the 3<sup>rd</sup> largest
cluster be compared to a permutation distribution obtained from just the 3<sup>rd</sup>
largest stat from each permutation?<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>The
answer to your specific question is “yes”.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
style='mso-list:Ignore'>4)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Our trials each have a baseline period – in order
to assess the differences between the two conditions, should we limit the
permutation distribution to stats selected just from the active periods of each
permutation?<o:p></o:p></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>You
can compare to a baseline that has the same number of samples as a data segment
obtained in some experimental condition.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Eric
Maris<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=NL style='font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Verdana","sans-serif";
color:#1F497D'>dr. Eric Maris<br>
Donders Institute for Brain, Cognition and Behavior<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Verdana","sans-serif";
color:#1F497D'>Center for Cognition and F.C. Donders Center for Cognitive
Neuroimaging<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Verdana","sans-serif";
color:#1F497D'>Radboud University</span><span style='font-family:"Verdana","sans-serif";
color:#1F497D'><br>
</span><span lang=EN-GB style='font-family:"Verdana","sans-serif";color:#1F497D'>P.O.
Box 9104</span><span style='font-family:"Verdana","sans-serif";color:#1F497D'><br>
</span><span lang=EN-GB style='font-family:"Verdana","sans-serif";color:#1F497D'>6500
HE Nijmegen<br>
The Netherlands<br>
T:+31 24 3612651<br>
Mobile: 06 39584581<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE style='font-family:"Verdana","sans-serif";
color:#1F497D'>F:+31 24 3616066<br>
E: e.</span><span lang=NL style='font-family:"Verdana","sans-serif";color:#1F497D'><a
href="mailto:e.maris@donders.ru.nl" title="blocked::mailto:maris@nici.kun.nl"><span
lang=DE>maris@donders.ru.nl</span></a></span><span style='font-family:"Verdana","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal>Thank you very much in advance!<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>__________________________________________________________________________________</span><o:p></o:p></p>
<p class=MsoNormal>Allen Ardestani Email: <a
href="mailto:aardesta@ucla.edu">aardesta@ucla.edu</a><o:p></o:p></p>
<p class=MsoNormal>Phone: (310) 825-5528<o:p></o:p></p>
<p class=MsoNormal>Medical Scientist Training Program<o:p></o:p></p>
<p class=MsoNormal>David Geffen School of Medicine at UCLA<o:p></o:p></p>
<p class=MsoNormal>Semel Institute for Neuroscience and Human Behavior<o:p></o:p></p>
<p class=MsoNormal>760 Westwood Plaza<o:p></o:p></p>
<p class=MsoNormal>Los Angeles, CA 90095-1759<o:p></o:p></p>
<p class=MsoNormal>USA<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p><span lang=NL>----------------------------------<o:p></o:p></span></p>
<p><span lang=NL>The aim of this list is to facilitate the discussion between
users of the FieldTrip toolbox, to share experiences and to discuss new ideas
for MEG and EEG analysis.<o:p></o:p></span></p>
<p><span lang=NL>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></span></p>
<p><span lang=NL>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></span></p>
<p>----------------------------------<o:p></o:p></p>
<p>The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.<o:p></o:p></p>
<p>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></p>
<p>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></p>
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<p>----------------------------------</p>
<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>