[Eeglablist] plotting and calculating stats on study difference waves
Makoto Miyakoshi
mmiyakoshi at ucsd.edu
Tue Apr 1 18:20:43 PDT 2014
Dear Alexandre,
I wrote a preliminary plugin for my colleagues who wants to perform simple
and flexible ERP studies on STUDY. Could you try std_ErpCalc from here, or
from your EEGLAB plugin manager system if you are using v13 or newer? Its'
under 'File'
http://sccn.ucsd.edu/wiki/Plugin_list_process
I don't use this plugin at all, so you may find problems. Please let me
know if you encounter troubles.
Makoto
2014-03-26 7:16 GMT-07:00 Alexandre Lehmann <alexandre.lehmann at umontreal.ca>
:
> 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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>>
>
>
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--
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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