<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi all,<div><br></div><div>sorry, I thought the answer would only go to Luisa. </div><div><br></div><div>Apologies,</div><div>Julian</div><div><br><div><div>Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
Hi all,<br>
<br>
First of all, @julian: It would be nice if you wrote in English so
that all people can understand what you are saying :)<br>
<br>
Second, I would like to mention ft_neighbourplot, which is a
relative new function and plots sensors and its' neighbours in 2D or
3D, depending on whether you got 2D or 3D coordinates. Using that
function, you can verify whether your neighbourselection looks
meaningful and makes sense.<br>
<br>
Finally, we are currently working on changing/improving the
neighbourselecion function. There will be different methods to
choose from, and we (me) will create templates for the most common
systems that can be used instead of relying on a particular
mathematical selection method. We will announce this when it's done
(probably soon).<br>
<br>
Maybe Julian is right and Luisa's problem is due to a 'wrong'
neighbourselection. Given that cfg.minnbhchan is set to 4, this
might be likely, because not all of the found clusters consist of 4
or more channels. What system are you using?<br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 5/16/2011 2:32 PM, Julian Keil wrote:
<blockquote cite="mid:DDE1521C-448B-4F10-83BA-E53104178BC9@gmail.com" type="cite">Hi Luisa,
<div><br>
</div>
<div>schnell from the top of my head: wie definierst du denn deine
neighbors?</div>
<div>Ich seh nirgendwo ein Feld cfg.neighbors....</div>
<div>Ich muss das bei unserem 4D-System immer angeben....</div>
<div>Es könnte sein, dass du die Struktur, welche Kanäle neben
welchen sind falsch definierst, so könntest du zu deinen
"random" Clustern kommen.</div>
<div><br>
</div>
<div>Ich mache diese Neighbor-Struktur folgendermaßen:</div>
<div><br>
</div>
<div>
<div>cfg=[]; </div>
<div>cfg.neighbourdist=0.1;</div>
<div>%cfg.grad=Comb_AV1_1{1}.grad;</div>
<div>cfg.layout='4D148.lay';</div>
<div>cfg.channel={'all'};</div>
<div>%cfg.grad.pnt=cfg.grad.pnt*100; </div>
<div>dummy=neighbourselection(cfg);</div>
<div><br>
</div>
<div>Da bekomme ich auch immer einen Output, wie viele Channels
so in der Umgebung sind (sollten in etwa 5 sein).</div>
<div><br>
</div>
<div>Hoffe das hilft dir weiter</div>
<div><br>
</div>
<div>Viele Grüße</div>
<div><br>
</div>
<div>Julian</div>
<div><br>
</div>
<div>
<div>Am 14.05.2011 um 22:37 schrieb Luisa Frei:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word;">Hi there,
<div>I am trying to compute a simple cluster-based
statistic in a between subjects design. I have followed
the steps in the respective tutorial very closely.</div>
<div>This the code I used:</div>
<div><br>
</div>
<div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg = [];</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.method = </font><font style="font: 12px Courier; color: rgb(160, 32,
240);" size="3" color="#a020f0" face="Courier">'montecarlo'</font><font style="font: 12px Courier;" size="3" face="Courier">;
</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.statistic = </font><font style="font: 12px Courier; color: rgb(160, 32,
240);" size="3" color="#a020f0" face="Courier">'indepsamplesT'</font><font style="font: 12px Courier;" size="3" face="Courier">; </font></div>
<div style="margin: 0px; min-height: 14px;"><font style="font: 12px Courier;" size="3" face="Courier"> </font><br class="khtml-block-placeholder">
</div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.correctm = </font><font style="font: 12px Courier; color: rgb(160, 32,
240);" size="3" color="#a020f0" face="Courier">'cluster'</font><font style="font: 12px Courier;" size="3" face="Courier">;</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.clusteralpha =
0.001; </font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.clusterstatistic
= </font><font style="font: 12px Courier; color:
rgb(160, 32, 240);" size="3" color="#a020f0" face="Courier">'maxsize'</font><font style="font:
12px Courier;" size="3" face="Courier">; </font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.minnbchan =
4; </font></div>
<div style="margin: 0px; min-height: 14px;"><font style="font: 12px Courier;" size="3" face="Courier"> </font><br class="khtml-block-placeholder">
</div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.tail = 0;
</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.clustertail =
0;</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.alpha =
0.005; </font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.numrandomization
= 500; </font></div>
<div style="margin: 0px; min-height: 14px;"><font style="font: 12px Courier;" size="3" face="Courier"> </font><br class="khtml-block-placeholder">
</div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">design =
[ones(1,13) ones(1,13)+1];</font></div>
<div style="margin: 0px; min-height: 14px;"><font style="font: 12px Courier;" size="3" face="Courier"> </font><br class="khtml-block-placeholder">
</div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.design =
design; </font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.ivar = 1;
</font></div>
<div style="margin: 0px; min-height: 14px;"><font style="font: 12px Courier;" size="3" face="Courier"> </font><br class="khtml-block-placeholder">
</div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.channel = {</font><font style="font: 12px Courier; color: rgb(160, 32,
240);" size="3" color="#a020f0" face="Courier">'MEG'</font><font style="font: 12px Courier;" size="3" face="Courier">,sub(1).allbadchan{:}};</font></div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">cfg.latency = [.15
.2];</font></div>
<div style="margin: 0px; min-height: 14px;"><font style="font: 12px Courier;" size="3" face="Courier"> </font><br class="khtml-block-placeholder">
</div>
<div style="margin: 0px;"><font style="font: 12px
Courier;" size="3" face="Courier">[stat] =
ft_timelockstatistics(cfg, grandavgG,grandavgE); %
individuals kept</font></div>
</div>
<div><font class="Apple-style-span" face="Courier">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div>
<div><font class="Apple-style-span" face="Courier"><br>
</font></div>
<div><font class="Apple-style-span" face="Arial">My
problem is, that I'm not sure which time resolution to
use. I would like to use a small resolution of 10 ms,
but this leads to a fairly random pattern of
significant sensors (see attached figure, on the
right). Of course, the more time points I include, the
less significant sensors are left over. However,
another problem is, that the ones that are left
(figure, left), are not related to big differences in
the activation pattern at all. How is it possible that
my significant sensors end up being so randomly
distributed? Also, ft_timelockstatistics only comes up
with one positive and one negative cluster., but the
sign. sensors are not always connected. Could anyone
give some helpful input here?</font></div>
<div><font class="Apple-style-span" face="Arial"><br>
</font></div>
<div><font class="Apple-style-span" face="Arial">Thanks,</font></div>
<div><font class="Apple-style-span" face="Arial">Luisa</font></div>
<div><font class="Apple-style-span" face="Arial"><br>
</font></div>
<div><font class="Apple-style-span" face="Arial">Fyi: I
have tried different thresholds and different numbers
of neighbourhood channels, but there's not much of a
change.</font></div>
</div>
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<br>
<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapitelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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