[Eeglablist] eeglablist Digest, Vol 89, Issue 31, -- 4. Re: baseline correction problem

Wed Mar 28 11:40:34 PDT 2012

Hello Marek
I have seen that when I use a small baseline interval (for example 50-100
msec) then i get these sifts in baseline you describe. But if I use a
baseline of greater length, this problem dissapears, in EEGLAB.

Maria Stavrinou
2012/3/27 <eeglablist-request at sccn.ucsd.edu>

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> Today's Topics:
>
>   1. Assoc. Development Engineer-- Swartz Center,      UC San Diego
>      (Scott Makeig)
>   2. Re: examples of how to get numerical data out of ERSP     and
>      specturm? (Arnaud Delorme)
>   3. Re: plot three groups in one panel (Arnaud Delorme)
>   4. Re: baseline correction problem (Arnaud Delorme)
>   5. Research position (PhD) in translational developmental
>      neuroscience (with a focus on eating disorders) (Bender, Stephan)
>
>
> ---------- Προωθούμενο μήνυμα ----------
> From: Scott Makeig <smakeig at ucsd.edu>
> To: eeglablist at sccn.ucsd.edu
> Cc:
> Date: Mon, 26 Mar 2012 15:46:54 -0700
> Subject: [Eeglablist] Assoc. Development Engineer-- Swartz Center, UC San
> Diego
> The Swartz Center for Computational Neuroscience, a center of the
> Institute for Neural Computation at the University of California at San
> Diego is soliciting applications for an open position as Associate
> Development Engineer. This person would be responsible for the development,
> integration, testing, and maintenance of state-of-the-art EEG and mobile
> brain/body imaging (MoBI) experimental systems and laboratory facilities,
> and would also function as data Laboratory Manager.  A more detailed job
> description (UCSD job #61615), list of qualifications, and application link
> may be found here<http://jobs.ucsd.edu/bulletin/job.aspx?cat=engineering&sortby=post&jobnum_in=61615>.
> The first round of applications will be evaluated 10 days from now.
>
> Scott Makeig
>
>
> --
> Scott Makeig, Research Scientist and Director, Swartz Center for
> Computational Neuroscience, Institute for Neural Computation, University of
> California San Diego, La Jolla CA 92093-0961, http://sccn.ucsd.edu/~scott
>
>
> ---------- Προωθούμενο μήνυμα ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To: Andrew Hill <andrewhill at ucla.edu>
> Cc: EEGLAB <eeglablist at sccn.ucsd.edu>
> Date: Mon, 26 Mar 2012 17:25:41 -0700
> Subject: Re: [Eeglablist] examples of how to get numerical data out of
> ERSP and specturm?
> Dear Andrew,
>
> the *erspdata* array in the call below
>
> *[STUDY erspdata ersptimes erspfreqs] =
> std_erspplot(STUDY,ALLEEG,'channels',{'Fp1'});*
>
> is a n x m cell array. n and m depend on your study design. To make it
> simple, create a very simple design with only 1 condition per subject (then
> n = 1 and m = 1) and erspdata will be a cell array of 1 x 1.
>
> The array in erspdata is for example 50 x 200 x 10. 50 frequencies, 200
> time points and 10 subjects/components. You may average the last dimension
> and export to a text file.
>
> *
> tmperspdata = mean(erspdata{1},3);
> save -ascii myfile.txt tmperspdata
>
> *
> Alternatively, you might want to preserve the subject/component
> information, so in this case, you would transform the ERSP 2-D image into a
> 1-D vector
>
>  *tmperspdata = reshape(erspdata{1},size(**erspdata{1},1)*size(**erspdata{1},2),
> size(**erspdata{1},3));*
> *save -ascii myfile.txt tmperspdata*
>
> Hope this helps,
>
> Arno
>
>  On Mar 19, 2012, at 2:26 PM, Andrew Hill wrote:
>
>  Hi Arno, and list.
>
> I'm still chasing the elusive extraction of numerical ERSP data.
>
> I'm able to get the times and frequencies out per the example below, but
> my "erspdata" is a 3 * 4 array of [4-D Double] structures, e.g. session *
> group.  Is there a straightforward way to export a summary of these to
> facilitate import into Excel, SPSS, etc?
>
> I've been spoiled by how much I can do with EEGLab without stellar matlab
> skills; any advice here is welcome :)
>
> Best,
> andrew
>
>
>  On May 25, 2011, at 10:04 PM, Arnaud Delorme wrote:
>
>  Dear Andrew,
>
> After plotting STUDY measures, look at the history
>
>  *STUDY = std_erspplot(STUDY,ALLEEG,'channels',{'Fp1'});*
>
> Then add output to the command line call (look up the function help for
> more information)
>
>  *[STUDY erspdata ersptimes erspfreqs] =
> std_erspplot(STUDY,ALLEEG,'channels',{'Fp1'});*
>
> Best,
>
> Arno
>
>  On Apr 28, 2011, at 1:48 PM, Andrew Hill wrote:
>
>  Hi folks,
>
> Can anyone give me an example of how to get numerical data out of ERSP or
> spectral computations?
>
> I've done a lot of "precompute channel measures" for STUDYs, but I'm not
> sure how to produce "numbers" instead of plots for ERSP, spectral, etc...
>
> I do see the command window output that says "Add output variables to
> command line call in history to retrieve results" but an example or two
> would go a long way to helping this less-than-expert Matlab user.
>
> Best,
> Andrew
>
>
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>
> ---------- Προωθούμενο μήνυμα ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To:
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Date: Mon, 26 Mar 2012 17:32:26 -0700
> Subject: Re: [Eeglablist] plot three groups in one panel
> Dear Muhammad,
>
> to plot the groups in the same panel, you need to change the ERP or
> spectrum plotting options. One option is "Plot first/second independent
> variable on the same panel". This is the option you might want to click.
> Hope this helps,
>
> Arno
>
>  On Mar 17, 2012, at 5:19 PM, Tarik S Bel-Bahar wrote:
>
>  consider plotting one figure at a time into bigger matlab figure with
> the subplot function.
>
>
>
>
> On Wed, Mar 14, 2012 at 7:57 AM, M Abul Hassan <abulhassan85 at yahoo.com>wrote:
>
>>   Dear list
>>
>> In a study that I have created has three groups with one condition. The
>> problem is that I could not be able to plot (spectrum, ERP) for all three
>> groups in one panel.
>>
>> Any suggestions would be greatly appreciated.
>>
>> Thanks
>> Best Regards
>> Muhammad Abul Hasan
>>
>>
>>
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>
> ---------- Προωθούμενο μήνυμα ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To: mirek <3mirek at gmail.com>
> Cc: eeglablist at sccn.ucsd.edu
> Date: Mon, 26 Mar 2012 17:37:45 -0700
> Subject: Re: [Eeglablist] baseline correction problem
> Dear Mirek,
>
> if you doubt about baseline correction, you can do baseline correction in
> every single dataset manually and then ignore the baseline correction
> option when you compute ERP at the STUDY level. You may also subtract
> components in individual datasets before computing ERPs in the STUDY
> interface. Finally, at the STUDY level, you can then plot the ERP of each
> individual subject. This way you might be able to resolve your dilemma and
> find out where the offset comes from.
> Hope this helps,
>
> Arno
>
> On Mar 24, 2012, at 4:12 PM, mirek wrote:
>
> > Hi all,
> >
> > The question seems to be quite basic, but still unresolved for me...
> >
> > I work (or trying to) using study/designs to compute and plot ERPs. The
> > problem is with the baseline. The plotted ERPs are definitely not
> > properly baseline corrected, however the prestimuls baseline interval is
> > set when precomputing channel measures (i.e.: "[-100 0]", since I need
> > -100 to 0 ms correction).
> >
> > I've checked whether the correction works to find out, that it does, but
> > in unpredictable (for me) manner. Depending on the interval I set for
> > correction, the ERPs are really moved up and down relative to x axis.
> > However, they are still not in the right place...
> >
> > My ERPs are segmented from -1000 to 2000 ms, artifactual ICs are marked
> > as bad and rejected in the stage of precomputing channel measures.
> >
> > I thought that it has something to do with artifactuals ICs which could
> > be removed AFTER baseline is corrected. However it is not the case,
> > since there is even more unpredictable offset at the posterior
> > electrodes, where artifacts (mostly ocular) are relatively weak.
> >
> > The same problem is visible for component cluster ERPs and it persists
> > with the EEGLAB 10 as well as 11.
> >
> > Any help...?
> >
> >
> > --
> > Mirek Wyczesany
> > Jagiellonian University
> > Psychophysiology Lab
> > Kraków, PL
> >
> >
> > PS. In the code of std_precomp I've found a remark at the 'rmbase'
> > parameter: "%deprecated, for backward compatibility purposes, not
> > documented"
> >
> > _______________________________________________
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>
>
>
>
> ---------- Προωθούμενο μήνυμα ----------
> From: "Bender, Stephan" <Stephan.Bender at uniklinikum-dresden.de>
> To: "'eeglablist at sccn.ucsd.edu'" <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Tue, 27 Mar 2012 19:05:20 +0200
> Subject: [Eeglablist] Research position (PhD) in translational
> developmental neuroscience (with a focus on eating disorders)
> ********
>
> *Research position (PhD) in translational developmental neuroscience
> (with a focus on eating disorders) *at the Department of Child and
> Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden
> University of Technology, Germany****
>
> ** **
>
> PLEASE REPOST FOR INTERESTED PARTIES****
>
> ** **
>
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>
> ** **
>
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>
> ** **
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>
> ** **
>
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>
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie
> ****
>
> Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden****
>
> E-Mail: KJPChefsekretariat at uniklinikum-dresden.de****
>
> ** **
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>
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>
> ** **
>
> ** **
>
> ** **
>
> Prof. Dr. med. Lic. psicología (UNED, ****Madrid****) Stephan Bender****
>
> Bereich Klinische Neurophysiologie und Multimodale Bildgebung****
>
> ** **
>
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie
> ****
>
> Telefon: ++49 351 458 7072****
>
> Fax:     ++49 351 458 5754****
>
> e-mail: Stephan.Bender at uniklinikum-dresden.de****
>
>  ****
>
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> an der Technischen Universität Dresden
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>
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-- 
-- 
Maria L. Stavrinou
MSc. PhD.
Postdoc Researcher
https://sites.google.com/site/marialstavrinou/
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