[Eeglablist] threshold option in std_plotcurve

Tue Feb 7 19:14:27 PST 2017

Dear Susanne,

Hmm honestly I don't have any experience in channel analysis on STUDY, so
hard to say.
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...

> 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.

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?

Makoto

On Sun, Feb 5, 2017 at 3:13 AM, Becker, Susanne <
susanne.becker at zi-mannheim.de> wrote:

> Dear Makoto,
>
> 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).
>
> I my STUDY I have 2 factors, one with 8 levels (different conditions in
> the task) and one with 2 levels (two drug conditions).
> 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:
>
> erp = STUDY.changrp(1,14).erpdata;
> erptimes = STUDY.changrp(1,14).erptimes;
>
>
> contrasts_6 = { erp{1,3};
>                 erp{1,4}};
>
>
> [F df pvals] = statcond(contrasts_6,'method', 'bootstrap'); % computes
> repeated measure ANOVA
>
>
> pvals = {pvals};
>
>
> std_plotcurve(erptimes, contrasts_6, 'plotconditions', 'together',
> 'plotstderr', 'on', 'figure', 'on', 'condstats', pvals, 'threshold',
> [NaN] )
>
>
> std_plotcurve(erptimes, contrasts_6, 'plotconditions', 'together',
> 'plotstderr', 'on', 'figure', 'on', 'condstats', pvals, 'threshold', 0.05
> )
>
>
> 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.
> The second std_plotcurve command stops with the error message described
> initially.
>
> Thanks very much for your help.
> Susanne
>
>
>
>
>
> *Von: * Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> *Betreff: **Aw: [Eeglablist] threshold option in std_plotcurve*
> *Datum: * 3. Februar 2017 19:51:56 MEZ
> *An: * "Becker, Susanne" <susanne.becker at zi-mannheim.de>
> *Kopie: * "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> *Antwort an: *<mmiyakoshi at ucsd.edu>
>
>
> Dear Susanne,
>
> > I saw that ‚g.maskarray‘ is also 150 columns long but has only one line.
> Might this somehow related to the error?
>
> That could be it.
> 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
>
> g.val2mask = g.val2mask(1,:);
>
> to make sure it works?
>
> 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?
>
> Makoto
>
>
> On Thu, Feb 2, 2017 at 11:50 AM, Becker, Susanne <
> susanne.becker at zi-mannheim.de> wrote:
>
>> Dear Makoto,
>>
>> thank you very much for our help. I’ll report the problem to the EEGLAB
>> Bugzilla in a second.
>>
>> 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?
>> If I just run the line (in debug mode):
>> find(g.val2mask < g.maskarray)
>>
>> I get this error mask, i.e. the same as when running the std_plotcurve
>> command.
>> Error using  <
>> Matrix dimensions must agree.
>>
>> Thanks
>> Susanne
>>
>>
>> Am 02.02.2017 um 20:30 schrieb Makoto Miyakoshi <mmiyakoshi at ucsd.edu>:
>>
>> Dear Susanne,
>>
>> Sorry for the trouble.
>> Could you report it to EEGLAB Bugzilla by filing the case? Those reports
>> submitted here will be directly read by developpers.
>> https://sccn.ucsd.edu/bugzilla/enter_bug.cgi
>> I appreciate your patience and cooperation.
>>
>> 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.
>>
>> Makoto
>>
>>
>>
>> On Thu, Feb 2, 2017 at 4:49 AM, Becker, Susanne <
>> susanne.becker at zi-mannheim.de> wrote:
>>
>>> Dear all,
>>>
>>> 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:
>>>
>>> std_plotcurve(erptimes, contrasts_5(:,1), 'plotconditions', 'together',
>>> 'plotstderr', 'on', 'figure', 'on', 'condstats', pvals, 'threshold',
>>> 0.05 )
>>>
>>> Calculating the stats before with:
>>> [F df pvals] = statcond(contrasts_5(:,1),'method', 'bootstrap‘);
>>>
>>> The error message I get is:
>>> Error using  <
>>> Matrix dimensions must agree.
>>>
>>> Error in plotcurve (line 104)
>>>                            Rregions  (find(g.val2mask < g.maskarray)) =
>>> 0;
>>>
>>> Error in std_plotcurve (line 400)
>>>                     plotcurve( allx, tmpdata{1}, 'colors', tmpcol,
>>> 'maskarray',
>>>                     tmpdata{2}, plotopt{3:end}, 'title',
>>> opt.titles{c,g});
>>>
>>> If I use NaN for the threshold option it works perfectly well. Can
>>> anybody tell me what I’m doing wrong?
>>> Best wishes
>>> Susanne
>>>
>>>
>>> -------------------------------------------------------
>>> Susanne Becker, PhD
>>> Head of Research Unit "Psychobiology of Pain“
>>>
>>> Department of Cognitive and Clinical Neuroscience
>>> Central Institute of Mental Health
>>> J5, 68159 Mannheim, Germany
>>> Phone: +49 (0)621 1703-6307 <+49%20621%2017036307>
>>> Fax: +49 (0)621 1703-6305 <+49%20621%2017036305>
>>> Email: susanne.becker at zi-mannheim.de
>>>
>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>>
>> -------------------------------------------------------
>> Susanne Becker, PhD
>> Head of Research Unit "Psychobiology of Pain“
>>
>> Department of Cognitive and Clinical Neuroscience
>> Central Institute of Mental Health
>> J5, 68159 Mannheim, Germany
>> Phone: +49 (0)621 1703-6307 <+49%20621%2017036307>
>> Fax: +49 (0)621 1703-6305 <+49%20621%2017036305>
>> Email: susanne.becker at zi-mannheim.de
>>
>>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
>
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>
> -------------------------------------------------------
> Susanne Becker, PhD
> Head of Research Unit "Psychobiology of Pain“
>
> Department of Cognitive and Clinical Neuroscience
> Central Institute of Mental Health
> J5, 68159 Mannheim, Germany
> Phone: +49 (0)621 1703-6307 <+49%20621%2017036307>
> Fax: +49 (0)621 1703-6305 <+49%20621%2017036305>
> Email: susanne.becker at zi-mannheim.de
>
>

-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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