[FieldTrip] When to detrend/demean

Mon Jan 7 21:07:49 CET 2013

Dear Ingrid and others,

I forgot to mention, the default has changed one year ago, according to the following thread on the list:

http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004666.html

Apologies for not having updated the FAQ. Ingrid, would you mind giving this a shot?

Best,

Jan-Mathijs

On Jan 7, 2013, at 8:31 PM, Ingrid Nieuwenhuis wrote:

> Hi Roemer,
> 
> Thanks for pointing to these questions. I'm a little bit confused about the default behavior with cfg.polyremoval as described there. So it seems the default of polyremoval for ft_freqanalysis is 1, meaning detrending always happens unless you specify otherwise, correct? So that means you don't have to call preprocessing with cfg.detrend = 'yes', correct? But you do have to specify cfg.demean = 'yes' in preprocessing? Or does removing the linear trend (which     is the default) in ft_freqanalysis automatically also demean the data? From the text under the figure in http://fieldtrip.fcdonders.nl/faq/why_does_my_tfr_look_strange it almost looks that way. Because it talks about cfg.polyremoval in the context of demeaning, not detrending. I don't find that text very clear by the way. Also, the title above the figure says "TFR before (left) and after (right) subtracting the DC component in the time domain", while when I look at the code it seems it should be "TFR of channel with large DC component (left) and channel without DC component (right) after ft_freqanalysis without demeaning". I'd be happy to update the FAQ, but first wanted to check whether I     understand correctly :)
> 
> Cheers,
> Ingrid
> 
> 
> On 1/7/2013 4:28 AM, Roemer van der Meij wrote:
>> Hi Vitoria,
>> 
>> I have only one thing to add to Ingrid's clear explanation. For frequency analysis, it's mostly a matter of noise. If you do not demean, the 0Hz been can bleed into all other frequency bins in a funny but patterned way. For detrending, the same story applies. When not detrending, the power of the center frequency of the linear trend (this frequency is very low), can bleed into other bins. 
>> 
>> The FAQs have two great example on this:
>> http://fieldtrip.fcdonders.nl/faq/why_does_my_tfr_look_strange
>> http://fieldtrip.fcdonders.nl/faq/why_does_my_tfr_look_strange_part_ii
>> 
>> Both are specific for when using 'mtmconvol' as frequency method (why this is so is explained shortly in the first FAQ), although in principle the issues could also occur using the other methods.
>> 
>> Hope it helps!
>> 
>> All the best,
>> Roemer
>> 
>> 
>> 
>> On Sun, Jan 6, 2013 at 3:24 AM, Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu> wrote:
>> Hi Vitoria,
>> 
>> The problem with these things is, it depends on what your interested in (hypothesis) and which methods you're using to analyze the data (ERP or frequanalysis, with our without ICA). All analysis steps have different pro and cons, so depending on your hypotheses and effects, what's good in one setup can be bad in the next. So you have to think of what the measures do, and how that effects your data.
>> 
>> But now for some answers :) I'm just using a lot of experience and some common sense, maybe people can add in some refs and math if they know :)
>> Demeaning just subtracts the mean of the specified time window (or indeed whole trial) from all samples
>> detrending removes linear trend (you can also remove higher order trends, just for completeness)
>> 
>> For ERPs you generally do want to demean using the baseline window, so the effect cancels out pre-stim. You don't want to detrend here, since often the ERP can have late components, and the signal might not be back to baseline yet. If you detrend in such a case, you will decrease the value samples late in the trials and increase the values during baseline. You will tilt the data (end down thus start up). But if you expect a linear trend due to equipment drift over longer time, that can muddle the ERP effect, then you might want to detrend. Also when the signal is noisy (high amplitude noise) at the end (due to speach artifacts), detrending might be dangerous.
>> 
>> For frequency analysis, demeaning has (as far as I know) no effect, since subtracting a constant does not change the frequency info in the signal. I know people do tend to detrend before freq analysis (so I also tend to do that),               but I have to admit, I don't know why really. Maybe to get rid of the drift, so it does not end up in the low frequencies. But again, the effect of detrending (which freqs it affects) depends how long your time window is, and which frequencies your interested in. If you are interested in really low frequencies, detrending might change your effects.
>> 
>> Hope this helps somewhat,
>> Ingrid
>> 
>> 
>> 
>> On 1/5/2013 2:21 AM, Vitória Magalhães Piai wrote:
>> 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
>> 
>> 
>> 
>> _______________________________________________
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>> 
>> -- 
>> Ingrid Nieuwenhuis PhD
>> Postdoctoral Fellow
>> Sleep and Neuroimaging Laboratory
>> Department of Psychology
>> University of California, Berkeley
>> California 94720-1650
>> Tolman Hall, room 5305
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> 
>> 
>> -- 
>> Roemer van der Meij M.Sc.
>> PhD Candidate
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognition
>> P.O. Box 9104
>> 6500 HE Nijmegen
>> The Netherlands
>> Tel: +31(0)24 3655932
>> E-mail: r.vandermeij at donders.ru.nl
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
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>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> -- 
> Ingrid Nieuwenhuis PhD
> Postdoctoral Fellow
> Sleep and Neuroimaging Laboratory
> Department of Psychology
> University of California, Berkeley
> California 94720-1650
> Tolman Hall, room 5305
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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