[Eeglablist] threshold option in std_plotcurve
Becker, Susanne
susanne.becker at zi-mannheim.de
Wed Feb 8 08:32:29 PST 2017
Dear Makoto,
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.
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?
Thanks!
Susanne
Am 08.02.2017 um 04:14 schrieb Makoto Miyakoshi <mmiyakoshi at ucsd.edu<mailto:mmiyakoshi at ucsd.edu>>:
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<mailto: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<mailto: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<mailto:susanne.becker at zi-mannheim.de>>
Kopie: "eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>" <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>>
Antwort an: <mmiyakoshi at ucsd.edu<mailto: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<mailto: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<mailto: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<mailto: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<tel:+49%20621%2017036307>
Fax: +49 (0)621 1703-6305<tel:+49%20621%2017036305>
Email: susanne.becker at zi-mannheim.de<mailto: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<tel:+49%20621%2017036307>
Fax: +49 (0)621 1703-6305<tel:+49%20621%2017036305>
Email: susanne.becker at zi-mannheim.de<mailto: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<tel:+49%20621%2017036307>
Fax: +49 (0)621 1703-6305<tel:+49%20621%2017036305>
Email: susanne.becker at zi-mannheim.de<mailto:susanne.becker at zi-mannheim.de>
--
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
Fax: +49 (0)621 1703-6305
Email: susanne.becker at zi-mannheim.de<mailto:susanne.becker at zi-mannheim.de>
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