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<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>Dear
Adrian,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>I am wondering if any of you have any advice or
experience adapting the methods of Maris et al. </span>(2007) to acute animal
recordings.<o:p></o:p></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>The basic problem is that we sample different locations on different
days, each yielding different trial numbers, and they certainly aren't 'the
same trial'.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>The simplest way to deal with this, as I see it, is as follows:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Carry out Maris et al. (2007) methods within each session, clustering
across time (we are working with dynamic spectra and coherencies), frequency,
and space. To correct for the multiple recording sessions, use a crude
bonferonni-corrected P-value as the threshold for the Monte-Carlo P value
(prcit/nsess) for identifying significant clusters. ((or correct the critical
value for establishing what the empirical clusters are initially))<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Is this unsound in any way? Any alternatives?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>The obvious drawbacks are having to introduce bonferroni-correction, as
well as losing sensitivity to weak effects seen in spatial proximity across
different sessions (i.e. the same guide tube position over many days).<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color=blue face="Times New Roman"><span
style='font-size:12.0pt;color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>A
lot can be said in response to your questions. Actually, it’s on my Todo
list to write a methodological paper about some of the issues that you raise. These
are the main points I can think about:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<ol style='margin-top:0cm' start=1 type=1>
<li class=MsoNormal style='color:blue;mso-list:l0 level1 lfo1'><font size=3
color=blue face="Bookman Old Style"><span lang=EN-GB style='font-size:
12.0pt;font-family:"Bookman Old Style"'> As your unit of observation,
you can choose for trials as well as sessions. If you choose for sessions,
then your dependent variable is an average over the trials within every
session.<o:p></o:p></span></font></li>
<li class=MsoNormal style='color:blue;mso-list:l0 level1 lfo1'><font size=3
color=blue face="Bookman Old Style"><span lang=EN-GB style='font-size:
12.0pt;font-family:"Bookman Old Style"'> If your unit of observation
is trials AND if there is heterogeneity across the different sessions,
then you should incorporate the variable SESSION as a blocking variable.
The theory of permutation tests also applies in the context of blocking
variables. I have added the blocking variable option in the statfuns for
testing regression coefficients. This was for a joint project with <st1:PersonName
ProductID="Vladimir Litvak," w:st="on">Vladimir Litvak,</st1:PersonName>
and the paper should be somewhere under review now. I have not yet added
it to the indepsamplesT and depsamplesT statfuns, but that shouldn’t
be too much of an effort.<o:p></o:p></span></font></li>
<li class=MsoNormal style='color:blue;mso-list:l0 level1 lfo1'><font size=3
color=blue face="Bookman Old Style"><span lang=EN-GB style='font-size:
12.0pt;font-family:"Bookman Old Style"'> The presence of effects that
are confined to a particular subvolume of the brain tissue from which you
sample, is a tricky one. Clustering in space definitely is an option, but the
current Fieldtrip code cannot deal with the fact that the different
recording sites were only partly sampled concurrently (because the probes
are lowered to different locations on different sessions), at least not in
a straightforward fashion. This differs from extracranial recordings in
which there is typically only a single recording session with a single channel
configuration.<o:p></o:p></span></font></li>
</ol>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>With
good Matlab programming skills, it is definitely possible to make the required
changes to the Fieldtrip code.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>Good
luck,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>dr.
<st1:PersonName ProductID="Eric Maris" w:st="on">Eric Maris</st1:PersonName><br>
Donders Institute for Brain, Cognition and Behavior<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>Center
for Cognition and <st1:place w:st="on"><st1:PlaceName w:st="on">F.C.</st1:PlaceName>
<st1:PlaceName w:st="on">Donders</st1:PlaceName> <st1:PlaceType w:st="on">Center</st1:PlaceType></st1:place>
for Cognitive Neuroimaging<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceName w:st="on"><font size=3
color=blue face="Bookman Old Style"><span lang=EN-GB style='font-size:12.0pt;
font-family:"Bookman Old Style";color:blue'>Radboud</span></font></st1:PlaceName><font
color=blue face="Bookman Old Style"><span lang=EN-GB style='font-family:"Bookman Old Style";
color:blue'> <st1:PlaceType w:st="on">University</st1:PlaceType></span></font></st1:place><br>
<st1:address w:st="on"><st1:Street w:st="on"><font color=blue
face="Bookman Old Style"><span lang=EN-GB style='font-family:"Bookman Old Style";
color:blue'>P.O. Box</span></font></st1:Street><font color=blue
face="Bookman Old Style"><span lang=EN-GB style='font-family:"Bookman Old Style";
color:blue'> 9104</span></font></st1:address><br>
<font color=blue face="Bookman Old Style"><span lang=EN-GB style='font-family:
"Bookman Old Style";color:blue'>6500 HE Nijmegen<br>
The <st1:place w:st="on"><st1:country-region w:st="on">Netherlands</st1:country-region></st1:place><br>
T:+31 24 3612651<br>
F:+31 24 3616066<br>
E: e.</span></font><font color=blue face="Bookman Old Style"><span
style='font-family:"Bookman Old Style";color:blue'><a
href="mailto:e.maris@donders.ru.nl" title="blocked::mailto:maris@nici.kun.nl"><span
lang=EN-GB>maris@donders.ru.nl</span></a></span></font><font color=blue
face="Bookman Old Style"><span lang=EN-GB style='font-family:"Bookman Old Style";
color:blue'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:blue'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'>MSc
Cognitive Neuroscience: </span></font><font size=1 color=blue face=Verdana><span
style='font-size:9.0pt;font-family:Verdana;color:blue'><a
href="http://www.ru.nl/master/cns/" title="http://www.ru.nl/master/cns/"><font
size=3 face="Bookman Old Style" title="http://www.ru.nl/master/cns/"><span
title="http://www.ru.nl/master/cns/"><span lang=EN-US style='font-size:12.0pt;
font-family:"Bookman Old Style"'>www.ru.nl/master/cns/</span></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 color=blue face="Bookman Old Style"><span
lang=EN-US style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=blue face="Bookman Old Style"><span
lang=EN-GB style='font-size:12.0pt;font-family:"Bookman Old Style";color:blue'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Any input on this would be greatly appreciated,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Thanks in advance.<br clear=all>
<br>
-- <br>
Adrian M. Bartlett, BA<br>
Neuroscience Graduate Diploma Program<br>
Graduate Program in Psychology<br>
Perception & Plasticity Laboratory<br>
Centre for Vision Research<br>
York University, Toronto, ON, Canada<br>
--<o:p></o:p></span></font></p>
</div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>----------------------------------<o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>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></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>http://www.ru.nl/fcdonders/fieldtrip/<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>