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Dear Makoto,
<div><br>
</div>
<div>unfortunately, GUI doesn’t support what I want to do for several reasons. First, I have more than 2 factors in my design (which I could get around by using subsets of the data in the STUDY and separate files), but more important and second, the contrast
I'm most interested in is a subtraction of two conditions, and, third, I really like the depiction with error bands around the curve, which is only available with the std_plotcurve command and not via the GUI.</div>
<div><br>
</div>
<div>I played around with the GUI a bit (using only two of my factors of interest) and realized that I’m not able to get the p-values plotted inside the plots (by setting the threshold option e.g to 0.05) and also that I’m not able to get the curves of my second
factor, which has two levels, overlaid in one plot. I don’t see a reason as I don’t get any error messages and do everything as described in the tutorial. But I guess this suggests that there is something wrong with my data or the STUDY setup. Do you have
any experience when such an error could occur?</div>
<div><br>
</div>
<div>Thanks!</div>
<div>Susanne</div>
<div><br>
</div>
<div>
<div>Am 08.02.2017 um 04:14 schrieb Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu">mmiyakoshi@ucsd.edu</a>>:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Dear Susanne,
<div><br>
</div>
<div>Hmm honestly I don't have any experience in channel analysis on STUDY, so hard to say.</div>
<div>Why do you need to use command line anyway? Doesn't GUI support what you want to do? If so, I wonder if you can try STUDY.history to obtain log of the executed code...</div>
<div><br>
</div>
<div>> when I delete one line of g.val2mask as you suggested, it runs through and plots a picture including the p-values indicated plot the line by black and white bars as expected.<br>
</div>
<div><br>
</div>
<div>This seems to suggest that something is wrong there, and erroneously two things are present. Without seeing actual code it's hard to say more than this. Any guess what these 'two things' correspond to, and how they should related to something else to make
it work?</div>
<div><br>
</div>
<div>Makoto</div>
<div><br>
</div>
<div><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Feb 5, 2017 at 3:13 AM, Becker, Susanne <span dir="ltr">
<<a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>Dear Makoto,<br>
<div><br>
</div>
<div>when I delete one line of g.val2mask as you suggested, it runs through and plots a picture including the p-values indicated plot the line by black and white bars as expected. However, the p-values are very different (not such a big surprise since I delete
this one line in g.val2mask).</div>
<div><br>
</div>
<div>I my STUDY I have 2 factors, one with 8 levels (different conditions in the task) and one with 2 levels (two drug conditions).</div>
<div>As I also want to plot some difference plot, I created a STUDY.design using the graphical interface including both my factors, computed the ERPs and computed all conditions using the GUI. Having the all the necessary information in memory, I used for example
this script:</div>
<div><br>
</div>
<div>
<div style="margin:0px;font-size:10px;font-family:courier">erp = STUDY.changrp(1,14).erpdata;</div>
<div style="margin:0px;font-size:10px;font-family:courier">erptimes = STUDY.changrp(1,14).erptimes;</div>
<div style="margin: 0px; font-size: 10px; font-family: courier; min-height: 12px;">
<br class="gmail-m_-6925190101101992737webkit-block-placeholder">
</div>
<div style="margin:0px;font-size:10px;font-family:courier">contrasts_6 = { erp{1,3};</div>
<div style="margin:0px;font-size:10px;font-family:courier"> erp{1,4}};</div>
<div style="margin: 0px; font-size: 10px; font-family: courier; min-height: 12px;">
<br class="gmail-m_-6925190101101992737webkit-block-placeholder">
</div>
<div style="margin:0px;font-size:10px;font-family:courier">[F df pvals] = statcond(contrasts_6,<span style="color:rgb(178,69,243)">'method'</span>,
<span style="color:rgb(178,69,243)">'bootstrap'</span>); <span style="color:rgb(37,153,45)">
% computes repeated measure ANOVA</span></div>
<div style="margin: 0px; font-size: 10px; font-family: courier; color: rgb(37, 153, 45); min-height: 12px;">
<br class="gmail-m_-6925190101101992737webkit-block-placeholder">
</div>
<div style="margin:0px;font-size:10px;font-family:courier">pvals = {pvals};</div>
<div style="margin: 0px; font-size: 10px; font-family: courier; min-height: 12px;">
<br class="gmail-m_-6925190101101992737webkit-block-placeholder">
</div>
<div style="margin:0px;font-size:10px;font-family:courier;color:rgb(178,69,243)">
<span style="">std_plotcurve(erptimes, contrasts_6, </span>'plotconditions'<span style="">,
</span>'together'<span style="">, </span>'plotstderr'<span style="">, </span>'on'<span style="">,
</span>'figure'<span style="">, </span>'on'<span style="">, </span>'condstats'<span style="">, pvals,
</span>'threshold'<span style="">, [NaN] )</span></div>
<div style="margin: 0px; font-size: 10px; font-family: courier; min-height: 12px;">
<br class="gmail-m_-6925190101101992737webkit-block-placeholder">
</div>
<div style="margin:0px;font-size:10px;font-family:courier;color:rgb(178,69,243)">
<span style="">std_plotcurve(erptimes, contrasts_6, </span>'plotconditions'<span style="">,
</span>'together'<span style="">, </span>'plotstderr'<span style="">, </span>'on'<span style="">,
</span>'figure'<span style="">, </span>'on'<span style="">, </span>'condstats'<span style="">, pvals,
</span>'threshold'<span style="">, 0.05 )</span></div>
<div style="margin: 0px; font-size: 10px; font-family: courier; min-height: 12px;">
<br class="gmail-m_-6925190101101992737webkit-block-placeholder">
</div>
<div style="margin:0px;min-height:14px">This is a very reduced version, since I tried to get it run with a very simple comparison. Here I want to compare one condition of the task (factor 1) between the two drug conditions (factor 2). The first std_plotcurve
command runs through and creates a figure with the two erps of the conditions and the exact p-values in an extra plot. These p-values are exactly the same comparted to when I plot pvals directly in a separate plot.</div>
<div style="margin:0px;min-height:14px">The second std_plotcurve command stops with the error message described initially.</div>
<div style="margin:0px;min-height:14px"><br>
</div>
<div style="margin:0px;min-height:14px">Thanks very much for your help.</div>
<div style="margin:0px;min-height:14px">Susanne</div>
<div style="margin:0px;min-height:14px"><br>
</div>
<div style="margin:0px;min-height:14px"><br>
</div>
<div style="margin:0px;min-height:14px"><br>
</div>
</div>
<div>
<div style="margin:0px;font-family:courier;min-height:14px"><br>
</div>
</div>
<br>
<blockquote type="cite">
<div style="margin:0px"><span style="font-family:helvetica;color:rgb(127,127,127)"><b>Von:
</b></span><span style="font-family:helvetica">Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br>
</span></div>
<div style="margin:0px"><span style="font-family:helvetica;color:rgb(127,127,127)"><b>Betreff:
</b></span><span style="font-family:helvetica"><b>Aw: [Eeglablist] threshold option in std_plotcurve</b><br>
</span></div>
<div style="margin:0px"><span style="font-family:helvetica;color:rgb(127,127,127)"><b>Datum:
</b></span><span style="font-family:helvetica">3. Februar 2017 19:51:56 MEZ<br>
</span></div>
<div style="margin:0px"><span style="font-family:helvetica;color:rgb(127,127,127)"><b>An:
</b></span><span style="font-family:helvetica">"Becker, Susanne" <<a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a><wbr>><br>
</span></div>
<div style="margin:0px"><span style="font-family:helvetica;color:rgb(127,127,127)"><b>Kopie:
</b></span><span style="font-family:helvetica">"<a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a>" <<a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a>><br>
</span></div>
<div style="margin:0px"><span style="font-family:helvetica;color:rgb(127,127,127)"><b>Antwort an:
</b></span><span style="font-family:helvetica"><<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br>
</span></div>
<div>
<div class="gmail-h5"><br>
<br>
<div dir="ltr">Dear Susanne,
<div><br>
</div>
<div>> I saw that ‚g.maskarray‘ is also 150 columns long but has only one line. Might this somehow related to the error?<br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">That could be it.</div>
<div class="gmail_extra">While using a debug mode and on the line of code you get error, can you delete one of the two lines in g.val2mask in this way</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">g.val2mask = g.val2mask(1,:);</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">to make sure it works?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Because I don't know anything about your STUDY design, I don't know what it means to have two lines in g.val2mask. Do you know what these two lines corresponds to your factorial design?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Makoto</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Feb 2, 2017 at 11:50 AM, Becker, Susanne <span dir="ltr">
<<a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a><wbr>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">Dear Makoto,
<div><br>
</div>
<div>thank you very much for our help. I’ll report the problem to the EEGLAB Bugzilla in a second.</div>
<div><br>
</div>
<div>I checked the length of 'Rregions‘ and ‚g.val2mask‘ using the debug mode. They are of the same length, both 150 columns with 2 lines each. However, I don’t know if it is relevant, I saw that ‚g.maskarray‘ is also 150 columns long but has only one line.
Might this somehow related to the error?</div>
<div>If I just run the line (in debug mode):</div>
<div>
<div>find(g.val2mask < g.maskarray)</div>
<div><br>
</div>
<div>I get this error mask, i.e. the same as when running the std_plotcurve command.</div>
<span class="gmail-m_-6925190101101992737gmail-">
<div>Error using < </div>
<div>Matrix dimensions must agree.</div>
</span></div>
<div><br>
</div>
<div>Thanks</div>
<span class="gmail-m_-6925190101101992737gmail-HOEnZb"><font color="#888888">
<div>Susanne</div>
</font></span>
<div>
<div class="gmail-m_-6925190101101992737gmail-h5">
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div>Am 02.02.2017 um 20:30 schrieb Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>>:</div>
<br class="gmail-m_-6925190101101992737gmail-m_4277365286538480162Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Dear Susanne,
<div><br>
</div>
<div>Sorry for the trouble.</div>
<div>Could you report it to EEGLAB Bugzilla by filing the case? Those reports submitted here will be directly read by developpers.</div>
<div><a href="https://sccn.ucsd.edu/bugzilla/enter_bug.cgi" target="_blank">https://sccn.ucsd.edu/bugzilla<wbr>/enter_bug.cgi</a><br>
</div>
<div>I appreciate your patience and cooperation.</div>
<div><br>
</div>
<div>Meanwhile, for the initial diagnosis... judging from the error message, 'Rregions' and 'g.val2mask' seem to have different length. Can you identify the size of these variables by using debug mode? If you can do it and the error is obvious, we may be able
to solve it by ourselves.</div>
<div><br>
</div>
<div>Makoto</div>
<div><br>
</div>
<div><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Feb 2, 2017 at 4:49 AM, Becker, Susanne <span dir="ltr">
<<a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a><wbr>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">Dear all,
<div><br>
</div>
<div>I’m using the std_plotcurve function to plot ERPs in two different conditions. I wanted to used the option „threshold“ with 0.05 as a significance threshold. However, when using the following commend I get an error message:</div>
<div><br>
</div>
<div><span style="font-family:courier;font-size:10px">std_plotcurve(erptimes, contrasts_5(:,1),
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'plotconditions'</span><span style="font-family:courier;font-size:10px">,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'together'</span><span style="font-family:courier;font-size:10px">,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'plotstderr'</span><span style="font-family:courier;font-size:10px">,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'on'</span><span style="font-family:courier;font-size:10px">,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'figure'</span><span style="font-family:courier;font-size:10px">,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'on'</span><span style="font-family:courier;font-size:10px">,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'condstats'</span><span style="font-family:courier;font-size:10px">, pvals,
</span><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'threshold'</span><span style="font-family:courier;font-size:10px">, 0.05 )</span></div>
<div><br>
</div>
<div>
<div>Calculating the stats before with:</div>
<div>
<div style="margin:0px"><font face="Courier" size="1">[F df pvals] = statcond(contrasts_5(:,1),</font><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'met<wbr>hod'</span><font face="Courier" size="1">,
</font><span style="font-family:courier;font-size:10px;color:rgb(178,69,243)">'bootstrap</span><font color="#b245f3" face="Courier" size="1">‘</font><font face="Courier" size="1">);</font></div>
</div>
<div style="margin:0px;font-size:10px;font-family:courier"><br>
</div>
<div style="margin:0px;font-size:10px;font-family:courier"><span style="font-family:helvetica;font-size:12px">The error message I get is:</span></div>
<div style="margin:0px">
<div style="margin:0px"><font face="Courier" size="1">Error using < </font></div>
<div style="margin:0px"><font face="Courier" size="1">Matrix dimensions must agree.</font></div>
<div style="margin:0px"><font face="Courier" size="1"><br>
</font></div>
<div style="margin:0px"><font face="Courier" size="1">Error in plotcurve (line 104)</font></div>
<div style="margin:0px"><font face="Courier" size="1"> Rregions (find(g.val2mask < g.maskarray)) = 0;</font></div>
<div style="margin:0px"><font face="Courier" size="1"><br>
</font></div>
<div style="margin:0px"><font face="Courier" size="1">Error in std_plotcurve (line 400)</font></div>
<div style="margin:0px"><font face="Courier" size="1"> plotcurve( allx, tmpdata{1}, 'colors', tmpcol, 'maskarray',</font></div>
<div style="margin:0px"><font face="Courier" size="1"> tmpdata{2}, plotopt{3:end}, 'title', opt.titles{c,g});</font></div>
</div>
<div><br class="gmail-m_-6925190101101992737gmail-m_4277365286538480162m_-3773384468181584508m_6596979020411048498webkit-block-placeholder">
</div>
<div>If I use NaN for the threshold option it works perfectly well. Can anybody tell me what I’m doing wrong?</div>
<div>Best wishes</div>
<div>Susanne</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
------------------------------<wbr>-------------------------<br>
Susanne Becker, PhD</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Head of Research Unit "Psychobiology of Pain“</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<br>
</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Department of Cognitive and Clinical Neuroscience<br>
Central Institute of Mental Health<br>
J5, 68159 Mannheim, Germany<br>
</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Phone: <a href="tel:+49%20621%2017036307" value="+4962117036307" target="_blank">
+49 (0)621 1703-6307</a></div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Fax: <a href="tel:+49%20621%2017036305" value="+4962117036305" target="_blank">+49 (0)621 1703-6305</a></div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Email: <a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a></div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" rel="noreferrer" target="_blank">
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To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail-m_-6925190101101992737gmail-m_4277365286538480162m_-3773384468181584508gmail_signature">
<div dir="ltr">Makoto Miyakoshi<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, University of California San Diego<br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
------------------------------<wbr>-------------------------<br>
Susanne Becker, PhD</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Head of Research Unit "Psychobiology of Pain“</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<br>
</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Department of Cognitive and Clinical Neuroscience<br>
Central Institute of Mental Health<br>
J5, 68159 Mannheim, Germany<br>
</div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Phone: <a href="tel:+49%20621%2017036307" value="+4962117036307" target="_blank">
+49 (0)621 1703-6307</a></div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Fax: <a href="tel:+49%20621%2017036305" value="+4962117036305" target="_blank">+49 (0)621 1703-6305</a></div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Email: <a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a></div>
</div>
</div>
</div>
<br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail-m_-6925190101101992737gmail_signature">
<div dir="ltr">Makoto Miyakoshi<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, University of California San Diego<br>
</div>
</div>
</div>
</div>
<br>
<br>
</div>
</div>
______________________________<wbr>_________________<br>
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Susanne Becker, PhD</div>
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Head of Research Unit "Psychobiology of Pain“</div>
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Department of Cognitive and Clinical Neuroscience<br>
Central Institute of Mental Health<br>
J5, 68159 Mannheim, Germany<br>
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Phone: <a href="tel:+49%20621%2017036307" value="+4962117036307" target="_blank">
+49 (0)621 1703-6307</a></div>
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Fax: <a href="tel:+49%20621%2017036305" value="+4962117036305" target="_blank">+49 (0)621 1703-6305</a></div>
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Email: <a href="mailto:susanne.becker@zi-mannheim.de" target="_blank">susanne.becker@zi-mannheim.de</a></div>
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</blockquote>
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-- <br>
<div class="gmail_signature">
<div dir="ltr">Makoto Miyakoshi<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, University of California San Diego<br>
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Susanne Becker, PhD</div>
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Head of Research Unit "Psychobiology of Pain“</div>
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Department of Cognitive and Clinical Neuroscience<br>
Central Institute of Mental Health<br>
J5, 68159 Mannheim, Germany<br>
</div>
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Phone: +49 (0)621 1703-6307</div>
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Fax: +49 (0)621 1703-6305</div>
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Email: <a href="mailto:susanne.becker@zi-mannheim.de">susanne.becker@zi-mannheim.de</a></div>
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