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<div style="direction: ltr;"><font face="Arial" style="color: rgb(0, 0, 0); font-size: 10pt;">Hi S. Baris Demiral,
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<div style="color: rgb(0, 0, 0); font-size: 10pt;"><font face="Arial">I have answers some of your questions, see below. Please note that it was difficult to answer all your questions because you didn't provide provide the actual code you used. Although your
description is helpful, being able to see the actual parameters you implemented, and the specific function (e.g, did you use ft_freqstatistics, and did you use ft_clusterplot?) make it easier for anyone in the community attempting to answer your questions. <span style="font-size:10pt">Please
see the FAQ for more details: http://fieldtrip.fcdonders.nl/faq/how_to_ask_good_questions_to_the_community</span><a href="http://fieldtrip.fcdonders.nl/faq/how_to_ask_good_questions_to_the_community" style="font-size:10pt" target="_blank">http://fieldtrip.fcdonders.nl/faq/how_to_ask_good_questions_to_the_community</a>.
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I'd like to point out that you can make good use of the search function (both inside FT - on the top right corner, and just on google), and reading the documentation for the functions that you are using, as many of your answers can be found there.</font></div>
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<div><font face="Arial" style="color: rgb(0, 0, 0); font-size: 10pt;">Finally, this FAQ should be of interest to you: </font><font face="Arial">http://fieldtrip.fcdonders.nl/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test</font></div>
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<div style="color: rgb(0, 0, 0); font-size: 10pt; font-family: Tahoma;">Best, </div>
<div style="color: rgb(0, 0, 0); font-size: 10pt; font-family: Tahoma;">Nietzsche</div>
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<font color="#000000" face="Tahoma" size="2"><b>From:</b> fieldtrip-bounces@science.ru.nl [fieldtrip-bounces@science.ru.nl] on behalf of Baris Demiral [demiral.007@gmail.com]<br>
<b>Sent:</b> 14 February 2015 17:58<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> [FieldTrip] Clustering algorithms, large and long clusters, and watershed?<br>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">Hi all,</div>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">I am testing clustering based correction algorithms on a TF power data in a predefined frequent band; theta. I have four conditions. I used F statistic. I defined neighbors moderately
so that the number of neighbors is not very small or extremely large. In some analyses I used pairwise t-test statistic to compare between conditions as well. I have a-priory expectations, such that some conditions will increase the centro-frontal theta, and
some will increase the posterior theta. I use maxsum and wcm approaches. </div>
<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'"><br>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">I heave the following questions:</div>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">-Why do I observe that very distant electrodes are clustered together? I noticed that FCZ is clustered with occipital electrodes and belong to the same cluster written as in stat.cfg.posclusterlabel
(label 1).</div>
<div style="color:rgb(0,0,0)"><font face="Arial" size="2">==> This could be due to the way your defined your neighbourhood structure. However, I can't make any conclusion from your defnition of "not very small or extremely large". Usually, when the neighbours
are defined it specifies the neighbourhood size in the matlab workspace, and it would also help to know what you specific for cfg.method, when calling ft_prepare_neighbours.<br>
<font size="2">==<font size="2">> It is important to note that <font size="2">even if there was a watershed method that it wouldn't answer the question of whether the centro-frontal theta is distinct from the occipital theta.
<font size="2">More generally, the use of cluster<font size="2">ing wo<font size="2">n't answer
<font size="2">this question either. It is better <font size="2">to use a feature in the
<font size="2">dat<font size="2">a e.g., power change<font size="2">, to determine whether the theta
<font size="2">differs between (groups of)<font size="2"> sensors.</font></font></font></font></font></font></font></font></font></font></font></font></font></font><br>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'"> In some ways I can understand that because my task produces highly posteriorized theta power. The centro-frontal power is weaker. This leads to my next question: "Is there a watershed
type of algorithm to separate these activities?" </div>
<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'"><br>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">- Are the electrodes I see in the plotting (marked by *,x,+) the peak electrodes in the clusters, or do these electrodes form the significant clusters (with smaller p values < .01,
.05 etc)?</div>
<div style="color:rgb(0,0,0)"><font face="Arial" size="2">==> I assume you are using ft_clusterplot, and in the documentation of this function it states that the "(default ['*','x','+','o','.'] for p < [0.01 0.05 0.1 0.2 0.3])"</font></div>
<div style="color:rgb(0,0,0)"><font face="Arial" size="2">==> Electrodes marked with the same symbol belong the the same cluster (whether they are significant depends on the symbol, or the way you've assigned what the symbols mean).</font></div>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'"> Because, if the cluster is formed between distant electrodes as mentioned above, I would expect to see the intermediate electrodes (such as CZ etc.) in the cluster electrode list
as well.</div>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">-Can you implement in plotting function where color can represent the cluster number? The *,+,x signs represent thresholds, but I cannot see which electrode belongs to which cluster.
If you color code electrodes, it will be very helpful. </div>
<div><font face="Arial" size="2">==> The elements in stat.poscluster/stat.negclusters are sorted according their p-values such that the cluster with the smallest p-value is first.<br>
==> Part of this tutorial also applies to TF data, it should help you with differentiating clusters (and not just using the symbols):<br>
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock<br>
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<div style="color:rgb(0,0,0)"><font face="Arial" size="2">The section of interest begins following text "<span style="line-height:22.5px; text-align:justify; background-color:rgb(255,255,255)">We now briefly discuss the configuration fields that are not specific
for </span><strong style="padding:0px; margin:0px; line-height:22.5px; text-align:justify; background-color:rgb(255,255,255)"><a href="http://fieldtrip.fcdonders.nl/reference/ft_timelockstatistics" class="wikilink1" style="padding:0px; margin:0px; color:rgb(0,136,204); text-decoration:none" target="_blank">ft_timelockstatistics</a></strong><span style="line-height:22.5px; text-align:justify; background-color:rgb(255,255,255)">:".<br>
<font size="2">==> I<font size="2"> <font size="2">cannot implement thi<font size="2">s feature, however, if you would<font size="2"> like to contribute to FT b<font size="2">y adding this functionality, you're welcome to
<font size="2">do so<font size="2"><font size="2">, see</font> http://fieldtrip.fcdonders.nl/contribute</font></font></font></font></font></font></font></font></span></font><br>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">-Is there a range of weight values for the weighted cluster mass (wcm) approach? I looked at the paper, and seems like 0.45-.055 seems to be the weight parameter. Is this correct?<br>
<font face="Arial" size="2">==> As a user, you need to determine and define a weight that is suitable for your data. The parameter to specify the weight is, cfg.wcm_weight.<br>
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<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">Thanks, </div>
<div style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'"> </div>
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<div class="gmail_extra" style="color:rgb(0,0,0); font-size:16px; font-family:'Times New Roman'">
-- <br>
<div class="gmail_signature">S. Baris Demiral<br>
NIH/NIDCD<br>
10 Center Drive<br>
Building 10, 5C410<br>
Bethesda, 20892<br>
MD</div>
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