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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Arno and all,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>First, thanks for the link to your book
chapter. It seems like something many people would find extremely useful.
Secondly, I would like to draw your attention to the fact that many permutation
methods for statistical analysis of EEG/MEG data are implemented in Fieldtrip
toolbox (<a href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a>)
in the clusterrandanalysis routine (<a
href="http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:reference:clusterrandanalysis">http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:reference:clusterrandanalysis</a>).
Fieldtrip is an open source Matlab toolbox with interface to EEGLAB (http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:integrating_with_eeglab).
</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Vladimir Litvak</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Technion – Israel Institute of
Technology</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 color=black
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;color:windowtext'>-----Original
Message-----<br>
<b><span style='font-weight:bold'>From:</span></b>
eeglablist-bounces@sccn.ucsd.edu [mailto:eeglablist-bounces@sccn.ucsd.edu] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Arnaud Delorme<br>
<b><span style='font-weight:bold'>Sent:</span></b> </span></font><font size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'>Sunday, March 05, 2006</span></font><font size=2
color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'> </span></font><font size=2 color=black face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;color:windowtext'>12:52 AM</span></font><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'><br>
<b><span style='font-weight:bold'>To:</span></b> Christopher Summerfield<br>
<b><span style='font-weight:bold'>Cc:</span></b> eeglab_maillist;
mfneelon@wisc.edu; wu xiang<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Eeglablist] ask
again about bootstrap and group analysis. pleasehelp</span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'>Dear all,<br>
<br>
I agree with Chris's description below. It is important to note that this is
not bootstrap but permutation statistics. Bootstraping would be a way to find
better confidence interval for the t-value BEFORE performing a parametric test
on it (comparing it to a table). Permutation statistics involve recomputing the
distribution of t-values using permutation of conditions (by the way, this does
not have necessarily to be a t-value and can be any distance measure between
the two distributions). This may also be generalized to more than two
conditions using ANOVA and reconstruvtion of the ANOVA distribution using
permutation of conditions. This is described with example page 19 in the
following document:<br>
<br>
</span></font><font face=Arial><span style='font-family:Arial'>Delorme, A.
(2005) Statistical methods. <i><span style='font-style:italic'>Encyclopedia of
Medical Device and Instrumentation</span></i>, in press. <a
href="http://www.sccn.ucsd.edu/%7Earno/mypapers/statistics.pdf" target="_blank">PDF
link</a>.</span></font><br>
<br>
A custom way to compensate for multiple comparisons is also described below:<br>
<br>
<font face=Arial><span style='font-family:Arial'>Tanji, K., Suzuki, F.,
Delorme, A., Shamoto, H., and Nakasato N. (2005) High-Frequency Gamma-Band
Activity in the Basal Temporal Cortex during Picture-Naming and
Lexical-Decision Tasks. <i><span style='font-style:italic'>J Neuroscience</span></i>,
25, 3287-3293. <a
href="http://www.jneurosci.org/cgi/content/full/25/13/3287?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=delorme&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1112980421492_6553&stored_search=&FIRSTINDEX=0&sortspec=relevance&journalcode=jneuro"
target="_blank">Journal's link</a>.<br>
<br>
Hope this helps,<br>
<br>
</span></font><font face=Arial><span style='font-family:Arial'>Arno</span></font><font
face=Arial><span style='font-family:Arial'><br>
</span></font><br>
Christopher Summerfield wrote: </p>
<pre style='margin-left:.5in' wrap=""><font size=2 color=black
face="Courier New"><span style='font-size:10.0pt'>dear wu xiang</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
.5in'><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>I think the procedure is outlined quite clearly in the Burgess & Gruzelier</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>article Phil Grieve just sent you, but to explain step by step...</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
.5in'><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>1) you have coherence estimates at p electrode pairs for s subjects in 2</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>conditions. This means that you can perform a t-test at each electrode.</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>If you have several estimates per pair, for example several time bins, or</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>perhaps even an entire time-frequency map, you may have several</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>t-estimates per pair. I will call these 'point estimate' statistics.</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
.5in'><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>2) at each pair, take your subject-condition assignments and swap them</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>1000 (or more times), recomputing your t-values at every pair or at every</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>timepoint or whatever. This will give you a null distribution</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>corresponding to every point estimate stat.</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
.5in'><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>3) you can then determine whether each point estimate falls within alpha</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>of its null distribution.</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
.5in'><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>4) to correct for multiple comparisons (for example, imagine that you have</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>20 electrodes=190 pairings), rather than checking each point estimate</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>against its distribution, enter (for each permutation) the maximum</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>statistic across your entire search space. So, in our example, if the</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>maximum permuted value from permutation 1 comes from electrode 188, you</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>enter that value into the null distribtuion. on the 2nd permutation, the</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>max value might come from another electrode. You then check all your</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>electrodes against this distribution. This will provide an 'familywise</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>error' correction for multiple comparisons.</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'> </span></font></pre><pre style='margin-left:
.5in'><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>good luck</span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>Chris</span></font></pre><pre style='margin-left:.5in'><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'> </span></font></pre><pre
style='margin-left:.5in'><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt'>_______________________________________________</span></font></pre><pre
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style='font-size:10.0pt'>eeglablist mailing list <a
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<p class=MsoNormal style='margin-right:0in;margin-bottom:12.0pt;margin-left:
.5in'><font size=3 color=black face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<div>
<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt'>-- <br>
<br>
</span></font><b><font size=4 face=Arial><span style='font-size:13.5pt;
font-family:Arial;font-weight:bold'>Arnaud Delorme, Ph.D.</span></font></b> <br>
<font size=4 color="#3333ff" face=Arial><span style='font-size:13.5pt;
font-family:Arial;color:#3333FF'>Swartz Center for Computational Neuroscience,</span></font><font
size=4 face=Arial><span style='font-size:13.5pt;font-family:Arial'> </span></font><font
size=4 color="#3333ff" face=Arial><span style='font-size:13.5pt;font-family:
Arial;color:#3333FF'>INC, University of San Diego California</span></font> <br>
La Jolla, CA92093-0961, USA </p>
<p style='margin-left:.5in'><b><font size=3 color=black face=Arial><span
style='font-size:12.0pt;font-family:Arial;font-weight:bold'>Tel</span></font></b><font
face=Arial><span style='font-family:Arial'> :<i><span style='font-style:italic'>(+1)-858-458-1927
ext 15</span></i></span></font> <br>
<b><font face=Arial><span style='font-family:Arial;font-weight:bold'>Fax</span></font></b><font
face=Arial><span style='font-family:Arial'> :<i><span style='font-style:italic'>(+1)-858-458-1847</span></i></span></font>
<br>
<b><font face=Arial><span style='font-family:Arial;font-weight:bold'>Web page</span></font></b><font
face=Arial><span style='font-family:Arial'>: <a
href="http://www.sccn.ucsd.edu/%7Earno">sccn.ucsd.edu/~arno</a></span></font> <br>
<b><font face=Arial><span style='font-family:Arial;font-weight:bold'>To think
upon</span></font></b><font face=Arial><span style='font-family:Arial'>:</span></font></p>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<p class=MsoNormal style='margin-right:0in;margin-bottom:12.0pt;margin-left:
.5in'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
font-family:Arial'>We have met the enemy, and he is us. </span></font></p>
<p class=MsoNormal style='margin-left:1.0in'><i><font size=3 color=black
face=Arial><span style='font-size:12.0pt;font-family:Arial;font-style:italic'>Walt
Kelly</span></font></i></p>
</blockquote>
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