[FieldTrip] A shifting power peak artefact

Mon Dec 12 09:14:42 CET 2022

Yes, thank you! Just to clarify, though, our baseline was not created by
zero-padding it was just a part of the segment used for demeaning and
detrending, its only definition was to start before the stimulus trigger,
but as we moved the epoch at exactly stimulus start, we could not demean
and detrend anymore because of how the script does it.

Am Mo., 12. Dez. 2022 um 09:03 Uhr schrieb Schoffelen, J.M. (Jan Mathijs)
via fieldtrip <fieldtrip at science.ru.nl>:

> Hi Ivo,
>
> In general, I think one should realise that the length of the data should
> be chosen long enough so that spectral components-of-interest can be
> reliably estimated. For low frequency bins this indeed would mean that the
> segments should be defined long enough. I don’t think that something that
> you call a ‘baseline’ is the correct way forward. One should not add any
> random (sub)segment of data to make it longer. Ideally, the signal
> component-of-interest should be switched on for the duration of the whole
> data segment for optimal sensitivity. Adding data with absent signal may
> increase your spectral resolution, but does not necessarily increase the
> sensitivity.
>
> Good luck discussing this with your colleagues,
>
> Jan-Mathijs
>
>
> Begin forwarded message:
>
> *From: *Ivaylo Iotchev <ivaylo.iotchev at gmail.com>
> *Subject: **Re: [FieldTrip] A shifting power peak artefact*
> *Date: *12 December 2022 at 08:51:43 CET
> *To: *"Schoffelen, J.M. (Jan Mathijs)" <
> janmathijs.schoffelen at donders.ru.nl>
>
> Dear Jan,
>
> thank you, indeed I discovered we made a more stupid mistake, since I
> followed my colleagues' suggestion to not define prestimulus for the
> segments (set to zero), but our demeaning and dentrending actually use/need
> that prestimulus-baseline. Now with the baseline back in and long enough
> epochs, the peaks of the 1/f and what seems our signal of interest separate
> from each other :) Let me know if this is something the forum should know,
> maybe such things get overlooked by others, my colleagues argument when we
> dived into the mistake was: This is not ERP, maybe we don't need the
> baseline. And I overlooked what the baseline was used for, because I am
> working on a different part of the same script... anyway, thank you!!
>
> Bests,
>
> Ivo
>
> Am Mo., 12. Dez. 2022 um 08:46 Uhr schrieb Schoffelen, J.M. (Jan Mathijs) <
> janmathijs.schoffelen at donders.ru.nl>:
>
>> Hi Ivo,
>>
>> Zero padding does not add information to your data, it only ensures that
>> the frequency bins of the FFT’ed signals end up at different locations of
>> the frequency axis. I don’t see why padding would affect the first energy
>> dense peak in the spectrum after DC correction.
>>
>> Multitapering implicitly assumes the spectrum to be locally white, if it
>> isn’t - i.e. most of the time - it’s not a big problem. However, it leads
>> to shifts in the peaks of truly bandlimited processes in the data, if those
>> band limited signal components are living on top of 1/f. Multitapering does
>> not minimize 1/f noise.
>>
>> Jan-Mathijs
>>
>>
>> On 10 Dec 2022, at 18:06, Ivaylo Iotchev <ivaylo.iotchev at gmail.com>
>> wrote:
>>
>> Although, dear Jan (anyone), if I can follow up with a secondary question
>> to your helpful answer.
>>
>> Reading the link you offered me I realized it is written with an approach
>> in mind, which I don't use. I saw on some examples of Fieldtrip scripts on
>> the official Fieldtrip pages, that you often define the cfg.foi relative to
>> an unpadded segment, e.g. 0.5 second long time-window is analyzed in steps
>> of 2 Hz and starting with 2 Hz. Would your text still explain my problem if
>> I use zero-padding to increase my resolution? More crucially, the position
>> of the main frequency being 1/segment length behaves as if my padding plays
>> no role, i.e. the segment length which determines the peak frequency is the
>> unpadded length.
>>
>> Finally, only if you have an idea, is the slepian sequence a legit way to
>> minimize 1/f noise? It seems to flatten the peak, but it also spreads out
>> the energy, and I wonder if that spread is itself noise or real signal that
>> was otherwise not visible.
>>
>> Thank you and sorry if I over-engage you on this one.
>>
>> Bests,
>>
>> Ivo
>>
>> Am Do., 8. Dez. 2022 um 10:04 Uhr schrieb Ivaylo Iotchev <
>> ivaylo.iotchev at gmail.com>:
>>
>>> Dankje wel!
>>>
>>> Am Do., 8. Dez. 2022 um 10:00 Uhr schrieb Schoffelen, J.M. (Jan Mathijs)
>>> via fieldtrip <fieldtrip at science.ru.nl>:
>>>
>>>> Hi Ivo,
>>>>
>>>> See: https://www.fieldtriptoolbox.org/faq/why_largest_peak_spectrum/
>>>> <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/faq/why_largest_peak_spectrum/__;!!HJOPV4FYYWzcc1jazlU!7hS8wc9fh7HjMyX-oGXc37ch6gH-QD6v1W_bkBQ-Tu4mHq5X1MMYl224IBtNAx3oFcIlBd77xBICILm6IAWPglCADnVGyZlJAvpwloM$>,
>>>> and https://www.fieldtriptoolbox.org/faq/why_does_my_tfr_look_strange/
>>>> <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/faq/why_does_my_tfr_look_strange/__;!!HJOPV4FYYWzcc1jazlU!7hS8wc9fh7HjMyX-oGXc37ch6gH-QD6v1W_bkBQ-Tu4mHq5X1MMYl224IBtNAx3oFcIlBd77xBICILm6IAWPglCADnVGyZlJ39orNSw$>
>>>>
>>>> Best wishes,
>>>> Jan-Mathijs
>>>>
>>>>
>>>>
>>>>
>>>> On 7 Dec 2022, at 14:40, Ivaylo Iotchev via fieldtrip <
>>>> fieldtrip at science.ru.nl> wrote:
>>>>
>>>> Dear community,
>>>>
>>>> I want to rephrase one of my questions without first emphasizing my own
>>>> theory of what is going on this time... what could cause the largest peak
>>>> in the data to invariantly be at the frequency which is 1/segment length?
>>>> That is, the peak is at 2 Hz when the segments are 0.5 seconds long... at 1
>>>> Hz when the segment is 1 second long etc. ...
>>>>
>>>> I previously hypothesized that something might be preventing Fieldtrip
>>>> from reading the sampling rate out of our data, but feel free to think
>>>> outside the box I offer you, much appreciated, thanks in advance!
>>>>
>>>> Bests,
>>>>
>>>> Dr. Ivaylo (Ivo) Iotchev
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>>>> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!9LhzA8TB3KE7n_eWe9D5PTqi5pVPMGBPv--HGNKtZG-6MCON-5NxvsMQXKI22KxcwEEcVPyAFMDyqUuYK1eg5x5RlsfCYk6CSCAeLQ$
>>>>
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>>>>
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>>
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