[FieldTrip] When to detrend/demean

[Stephen Politzer-Ahles]

Hi Vitoria,

This is not exactly my area of expertise, but I just wanted to point
out that in other speech production ERP research I'm familiar with
(such as bereitschaftspotential experiments--e.g. McArdle et al.,
2009, in Clinical Neuropsychology), a baseline period somewhere before
the onset of motor activity is used. (For instance, that paper used
[-3 -2.5] relative to the onset of articulator movement.)

However, if you're using ICA, there is an argument that ICA does
better when you use the whole epoch as the baseline (or at least use a
pretty long baseline) or do no baseline correction at all (David
Groppe has a paper on this, Groppe et al. 2009 in NeuroImage); see
e.g. http://sccn.ucsd.edu/pipermail/eeglablist/2010/003539.html.

Best,
Steve Politzer-Ahles

-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/


> Message: 4
> Date: Sat, 05 Jan 2013 11:21:34 +0100
> From: Vit?ria Magalh?es Piai  <vitoria.piai at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] When to detrend/demean
> Message-ID: <50E7FEAE.3080103 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear ftrippers,
>
> I'm having a discussion with a colleague on something that is still a
> bit unclear to us. Since I trust the knowledge going around here a lot,
> I thought it would be my best chance to get a good answer: When should
> we demean/detrend?
>
> As relevant background, our EEG datasets involve speech production on
> every trial.
> We read in the data, use ft_databrowser to mark the artefacts and then
> do complete artefact rejection with ft_rejectartifact. The trials often
> include speech (onset).
> I see in the tutorial that the cfg for preprocessing is pretty simple,
> and ft_preprocessing default has no detrend/demean.
> But in the FT example 'Reading and pre-processing EEG data', the cfg is
>
> cfg.demean           = 'yes';
> cfg.baselinewindow  = [-0.2 0];
>
>
> In my data, I used cfg.demean = 'yes'; with no cfg for the baseline
> window because I don't want to correct the signal with a specific
> interval (and I assume this will take the whole segment then).
> Our concern is that, given that people speak during part of the trial
> (always towards the end), using demean here is not a good idea (the
> signal changes induced by moving the jaws, etc., are included in the
> calculation). Is this necessarily the case or can it be fixed with
> subsequent computations (see below)? Do I need to go through artefact
> rejection again? My guess would be that the damage caused by having
> demean here doesn't change that much where the eyeblinks are and I
> always take quite broad windows to mark the artefacts, so at least for
> the AR I should be safe, but I'd like to check that with you guys.
>
> Then, when calculating ERPs, I had both demean and detrend before
> timelocking.
> But for the TFRs, I didn't do any of these (dunno why). I'm using the
> ft_freqanalysis after the 2011 change (removing the first order linear
> trend from the time domain data).
> Do I need to redo my TFRs or is it enough if I do sanity checks and
> everything is in place (like visual alpha and gamma, etc.)?
>
> And my last question, for once and for all, so that I get it right next
> time from the start (assuming that I'll always have EEG speech
> production data with ERPs and TFRs analysed). Is this the best way to do it?
> - preprocess with default (so NO detrend and NO demean)
> - then demean and detrend for ft_timelockanalysis and ft_freqanalysis
>
> Thanx a lot, and (keeping to the Dutch tradition) all the best for 2013!
> Vitoria