[FieldTrip] When to detrend/demean

Ingrid Nieuwenhuis inieuwenhuis at berkeley.edu
Mon Jan 7 22:53:19 CET 2013


Thanks JM, all clear now. FAQ updated: Done!
Cheers,
Ingrid

On 1/7/2013 12:07 PM, jan-mathijs schoffelen wrote:
> 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 <mailto: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
>>>
>>>
>>>
>>>         _______________________________________________
>>>         fieldtrip mailing list
>>>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>         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 <mailto: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 <mailto:r.vandermeij at donders.ru.nl>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> 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
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> 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

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