[FieldTrip] What kind of baseline correction to use for time-frequency analysis

Esther Eijlers eijlers at rsm.nl
Tue Jun 17 13:44:57 CEST 2014


Dear Jorn,

Thanks a lot for the clarification!

Best,
Esther

On 17/06/14 09:46, ""Jörn M. Horschig"" <jm.horschig at donders.ru.nl> wrote:

>Hi Esther,
>
>>  1. If I understand it correctly, with the default config setting for
>>     cfg.polyremoval the mean of the whole trial is subtracted (prior
>>     to spectral analysis) to get rid of the offset in oscillations.
>>
>'Getting rid of the offset in oscillations' is not the purpose of
>demeaning prior to doing a frequency analysis. See here:
>http://fieldtrip.fcdonders.nl/faq/why_does_my_tfr_look_strange
>
>>  1. Does it mean that since I¹m doing analyses on a participant level
>>     first, I only need to do this kind of baseline correction (from
>>     stimulus onset on)?
>>
>
>No, this is not a baseline correction as you are thinking of here.
>Remember that a power spectrum is obtained by squaring the fourier
>coefficients, i.e. power is always positive. Also, you want to baseline
>correct per frequency, because of the 1/f characteristic.
>
>>  1. I thought that I should /not/subtract the mean of a window prior
>>     to stimulus onset, from the raw trial data before doing
>>     time-frequency analysis (the kind of baseline correction you would
>>     do with ERP analyses), but I see this happening in some articles.
>>     Did I not get it right, or is this related to the distinction
>>     between evoked and induced power, or something else?
>>
>As mentioned in the link above, you should demean the whole trial in
>FieldTrip because of the way the mtmconvol method is implemented. Any
>other "baseline correction" in the time-domain will only affect the DC
>bin (ie 0Hz), but not the estimatoin at individual frequencies. This is
>because baseline correction in the time-domain is a mere subtraction of
>a your data by a single number. Hence, the frequency content of your
>data stays unchanged.
>
>>  1. Or is it an option (and should I) subtract the mean of a window
>>     prior to stimulus onset only after decomposition of the data in
>>     the power spectrum, for all trials?
>>
>Yes, in any plotting function, you can set cfg.baseline and
>cfg.baselinetype. You can also call ft_freqbaseline. Note baselining is
>also not a trivial thing here. You can serious harm (i.e. invalidate)
>your statistics if you're doing it wrong (but that depends on your
>experimental design and question). Usually, if you compare conditions
>you should not do a baseline correction at all (otherwise any
>statistical difference might show up due to a difference in baseline to
>start with).
>
>Best,
>Jörn
>
>On 6/16/2014 4:35 PM, Esther Eijlers wrote:
>> Dear community,
>>
>> Although I¹ve seen other questions related to this topic, I still have
>> some questions regarding baseline correction when executing a
>> time-frequency analysis:
>>
>> After time-frequency analysis, I want to use the trial output either
>> to compare (within participants) trials from different conditions or
>> to put the datapoints of different trials into a regression (also on
>> participant level).
>> The question for me is how to deal with a baseline correction in this
>> situation? The data before each trial of interest is in reaction to
>> viewing a fixation cross.
>>
>>  1. If I understand it correctly, with the default config setting for
>>     cfg.polyremoval the mean of the whole trial is subtracted (prior
>>     to spectral analysis) to get rid of the offset in oscillations.
>>  2. Does it mean that since I¹m doing analyses on a participant level
>>     first, I only need to do this kind of baseline correction (from
>>     stimulus onset on)?
>>  3. I thought that I should /not/subtract the mean of a window prior
>>     to stimulus onset, from the raw trial data before doing
>>     time-frequency analysis (the kind of baseline correction you would
>>     do with ERP analyses), but I see this happening in some articles.
>>     Did I not get it right, or is this related to the distinction
>>     between evoked and induced power, or something else?
>>  4. Or is it an option (and should I) subtract the mean of a window
>>     prior to stimulus onset only after decomposition of the data in
>>     the power spectrum, for all trials?
>>
>> Thanks a lot!
>>
>> Best,
>> Esther
>>
>>
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>>
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>
>
>--
>Jörn M. Horschig
>PhD Student
>Donders Institute for Brain, Cognition and Behaviour
>Centre for Cognitive Neuroimaging
>Radboud University Nijmegen
>Neuronal Oscillations Group
>FieldTrip Development Team
>
>P.O. Box 9101
>NL-6500 HB Nijmegen
>The Netherlands
>
>Contact:
>E-Mail: jm.horschig at donders.ru.nl
>Tel:    +31-(0)24-36-68493
>Web: http://www.ru.nl/donders
>
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