[Eeglablist] plotting and calculating stats on study difference waves

[Alexandre Lehmann]

Hello,

I am again confronted to the problem of wanting to use STUDY structure and
compute difference waves and compare those differences. I am wondering
whether since this 2011 post there has been new development in either
EEGLAB or ERPLAB that allow to more easily compute, plot and perform stats
on difference waves ?

I just read that since EEGLAB v13 one can use a custom function to be
performed on each data set of the study in std_precomp but I am not really
sure how I would use it for that purpose.

Any hints and tips are welcome !
If not I guess I'll stick to Hamish Innes-Brown's workaround described
below.

Best

A.


On Tue, Jun 28, 2011 at 7:47 PM, Hamish INNES-BROWN <
HINNES-BROWN at bionicsinstitute.org> wrote:

> Hi Alexandre, I have thought about using ERPLAB, but as you say, the group
> analysis/stats is much better in EEGLAB, as long as you don't need to do
> any subtractions...  In ERPLAB, as far as I can see the subtraction is
> handled easily, but then you need to do the stats and plotting externally
> anyway (back in matlab, or SPSS, signaplot etc), so I figured it would be
> easier just to do the subtraction in matlab/EEGLAB anyway, and then figure
> out how to send the results to the EEGLAB plotting and stats functions.
>
> I have a solution, but it's not very elegant. I have four conditions (A1
> A2 B1 B2), and want to calculate DIFF1 = A2 - A1, and DIFF2 = B2 - B1, and
> then do plots and stats on DIFF1 vs DIFF2
>
> 1) Proceed as if making an "old-style" (before the STUDY.design feature)
> study. IE epochs for each condition are saved in separate .set files.
> 2) Loop though all the set files, making an EEG.erp variable, which is
>  mean(EEG.data, 3).  You might need to make that double(mean(EEG.data,3))
> if you have previously used the option to use single precision only in the
> options.eeg file.
> 3) Now you have an ERP in each set file, one for each subject and
> condition.
> 4) Now make separate STUDYs for A1 and A2, and B1 and B2 (2 studies, with
> 2 conditions in each - STUDYA and STUDYB).  Then if you like you can get
> plots and stats of A1 vs A2 and B1 vs B2.
>
> 5) Load STUDYA, and make a loop doing the subtraction as follows:
>
> >       for ss = 1:length(STUDY.subject)
> >               erp_DIFFA(:,:,ss) = EEG(ss*2).erp  - EEG((ss*2)-1).erp;
> >       end
>
> This will subtract all the odd (which should be A1) from even (A2) ERPs
> you previously made.
>
> 6) Do the same for STUDYB
>
> You then have a matrix (time, chans, subjects) for DIFFA and DIFFB.  To
> get the grand average you just get the mean across the third dimension.
>
> DIFFA (time, chans, ss)
> DIFFB (time, chans, ss)
>
> > GAVG_A = mean(DIFFA, 3);
> > GAVG_B = mean(DIFFB, 3);
>
>
> 7) Then to get the nice plots and stats from the STD functions is a bit
> tricky. You no longer have these DIFF waves in the STUDY structure, so you
> cannot use the GUI, and have to fiddle around to get the data in a format
> that the STD functions like.  I have only just worked this out so some
> things could be wrong, but what I have done is set up DIFFA and DIFFB in a
> cell array like this:
>
> > erpdata  = {DIFFA;  DIFFB};
>
> Then I have used
> > pvals = std_stat(erpdata, 'option', 'value');   to calculate stats
> between DIFFA and DIFFB.
>
> The you feed those pvals into the plotting function:
> > std_plotcurve(times, erpdata, 'condstats', pvals, 'endless', 'options',
> 'go', 'here');
>
> And if you give that the right options and channel locations, you will get
> a head-shaped plot of your XX channels, with two lines per plot (one for
> each difference wave), and the grey boxes indicating the significant
> differences.
>
>
> I hope that is of some help, however I suspect some of the more
> experienced users might be cringing at this, it's probably not the most
> efficient way...   Probably there is a way to use STUDY.design for instance.
>
> -hamish-
>
>
>
>
>
> -----Original Message-----
> From: alexandre.lehmann at gmail.com [mailto:alexandre.lehmann at gmail.com] On
> Behalf Of Alexandre Lehmann
> Sent: Tuesday, 28 June 2011 1:59 AM
> To: Hamish INNES-BROWN
> Subject: Re: [Eeglablist] plotting and calculating stats on study
> difference waves
>
> Hello Hamish,
>
> I also have trouble comparing difference waves, I couldn't find any clean
> way to do it.
> I am now trying to do it with ERPLAB which easily allows to compute and
> plot difference waves.
>
> http://www.erpinfo.org/erplab/erplab-documentation/erplab-manual/Bin_Operations.htm
>
> What I haven't found out yet is whether it offers the same powerful group
> analysis as the STUDY does.
>
> Looking forward to knowing if you found another more practical solution,
>
> Regards
>
> --
> Alexandre Lehmann, Phd
> Postdoctoral research fellow
> Laboratory for Brain, Music & Sound Research BRAMS - Université de
> Montréal Pavillon 1420 boul. Mont Royal Case Postale 6128, Station
> Centre-Ville Montreal (QC)  H3C 3J7
>
>
> On Sun, Jun 19, 2011 at 9:13 PM, Hamish INNES-BROWN
> <HINNES-BROWN at bionicsinstitute.org> wrote:
> > Sorry for re-posting but I realised the last time I posted this in HTML
> format and it got scrubbed..
> >
> >
> > Hello again, I have recently been working with two STUDYs (12 subjects,
> two conditions in each study) in which I have calculated some new data for
> each participant and condition (MGFP), as well as calculated a difference
> ERP and difference MGFP between the two conditions.
> >
> > So I have:
> > STUDY1 - cond1 & cond2, calculated DIFF1
> > STUDY2 - cond3 & cond4, calculated DIFF2
> >
> > My general approach has been
> > 1.      Load STUDY 1 and calculate the ERP for each condition (I have
> actually done this by looping through an EEG(x).erp variable I inserted
> earlier, though I now realise I could have got the same info more easily
> from STUDY.changrp.erpdata)
> > 2.      Do the subtraction DIFF1 = ERPcond2 - ERPcond1
> > 3.      Load STUDY 2 and do the same
> >
> > I'm then left with DIFF1 and DIFF2 (each 60 elecs x 500 pts x 12 ss)
> >
> > What I'd like to do is use the std_erpplot function to plot, compare and
> do the stats on these two new waves, but I don't have the a whole new
> 'STUDY' structure to go with them. Looking at the the help for std_erpplot
> it looks like you do need a STUDY as an input.
> >
> > I then had a look through std_erpplot.m to see if I could find an
> internal plotting function that could work with a [elecs, points, ss]
> matrix,  and I found std_plotcurve. Am I heading in the right direction?
> >
> >
> >
> >
> >
> >
> > Hamish Innes-Brown
> > Research Assistant
> > The Bionics Institute of Australia
> >
> > t: +61 3 9667 7529
> > f: +61 3 9667 7518
> > e: hinnes-brown at bionicsinstitute.org
> > w: http://www.bionicsinstitute.org/profiles/HamishInnes-Brown.html
> > w2: http://musicalbionics.wordpress.com/
> >
> > 2nd International Medical Bionics Conference, Phillip Island, 20-23 Nov
> 2011
> > http://www.iceaustralia.com/medicalbionics2011/
> >
> >
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