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<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>Dear Sameer,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> 1) cfg.onetwo = 'onesided_2<1' vs
cfg.onetwo = 'onesided_1<2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> >From my understanding, it seems that one
sided tests only look for<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> positive clusters i.e. the test statistic higher
than cfg.alphathresh.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> Thus clusters showing up as posclusters for
coherence difference in one<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> case should not show up at all in the other. Yet,
both the tests seem to<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> give me same clusters.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>If this is the case, then there is an error in the
code. Can you send me your config and screen output of clusterrandanalysis?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> 2) using cfg.onetwo = twosided I should get
clusters which in some<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> way are union of the two sets above. Yet, I seem
to get completely<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> different clusters, sometimes with nothing in
common between twosided and<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> onsesided tests.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'>The clusters with the
twosided-option should NOT be the union of the clusters with the two onesided
options. This is because the thresholding values with the twosided-option are
at cfg.alphathresh/2 and (1-cfg.alphathresh/2), whereas for the two onesided
options they should be at, respectively, cfg.alphathresh and (1-cfg.alphathresh).<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> 3) Most clusters I find seem to have a high
p-value. Would the<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> confidence increase if I use a different
alphathresh which I think is used<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> for thresholding the Z-statistic for defining
clusters. (I just realized<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> that I neglected to define cfg.alphathresh and
though I could not find a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> default value used in clusterandanalysis, the
program is obviously using<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> some).<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'>On the basis of my experience, I
do not expect a substantial influence of the cfg.alphathresh value on the
p-values.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 color=black face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> 4) What is the motivation behind cfg.minnbchan
? Should it be based<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>> upon the neurobiological effect I am investigating?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt'>The motivation behind cfg.minnbchan is that some
samples (i.e., channel-frequency-pairs or channel-frequency-time-triplets) with
a big sample-specific statistic may have a few neighbouring samples with also a
big sample-specific statistic, just by chance. To "prune out" these
chance connections, set cfg.minnbchan high (e.g., 3).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>Kind regards,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>Eric Maris<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>dr. <st1:PersonName
tabIndex="0"
style="BACKGROUND-POSITION: left bottom; BACKGROUND-IMAGE: url(res://ietag.dll/#34/#1001); BACKGROUND-REPEAT: repeat-x"
w:st="on">Eric Maris</st1:PersonName><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>NICI/Biological
Psychology and<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceName w:st="on"><font size=3
face="Bookman Old Style"><span lang=EN-US style='font-size:12.0pt;font-family:
"Bookman Old Style"'>F.C.</span></font></st1:PlaceName><font
face="Bookman Old Style"><span lang=EN-US style='font-family:"Bookman Old Style"'>
<st1:PlaceName w:st="on">Donders</st1:PlaceName> <st1:PlaceType w:st="on">Center</st1:PlaceType></span></font></st1:place><font
face="Bookman Old Style"><span lang=EN-US style='font-family:"Bookman Old Style"'>
for Cognitive NeuroImaging<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=3
face="Bookman Old Style"><span lang=EN-US style='font-size:12.0pt;font-family:
"Bookman Old Style"'>University</span></font></st1:PlaceType><font
face="Bookman Old Style"><span lang=EN-US style='font-family:"Bookman Old Style"'>
of <st1:PlaceName w:st="on">Nijmegen</st1:PlaceName></span></font></st1:place><font
face="Bookman Old Style"><span lang=EN-US style='font-family:"Bookman Old Style"'><o:p></o:p></span></font></p>
<p class=MsoNormal><st1:address w:st="on"><st1:Street w:st="on"><font size=3
face="Bookman Old Style"><span lang=EN-US style='font-size:12.0pt;font-family:
"Bookman Old Style"'>P.O. Box</span></font></st1:Street><font
face="Bookman Old Style"><span lang=EN-US style='font-family:"Bookman Old Style"'>
9104</span></font></st1:address><font face="Bookman Old Style"><span
lang=EN-US style='font-family:"Bookman Old Style"'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>6500 HE Nijmegen<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>The <st1:country-region
w:st="on"><st1:place w:st="on">Netherlands</st1:place></st1:country-region><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>T:+31 24 3612651
(NICI)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>T:+31 24 3610754
(FCDC)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span
style='font-size:12.0pt;font-family:"Bookman Old Style"'>F:+31 24 3616066
(NICI)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span
style='font-size:12.0pt;font-family:"Bookman Old Style"'>E: maris@nici.ru.nl<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Bookman Old Style"><span lang=EN-US
style='font-size:12.0pt;font-family:"Bookman Old Style"'>MSc Cognitive
Neuroscience :</span></font><font size=1 face=Verdana><span style='font-size:
9.0pt;font-family:Verdana'><a href="http://www.ru.nl/master/cns/"
title="http://www.ru.nl/master/cns/"><font size=3 face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;font-family:"Bookman Old Style"'>www.ru.nl/master/cns/</span></font></a></span></font><font
size=1 face=Verdana><span lang=EN-US style='font-size:9.0pt;font-family:Verdana'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></font></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>