[FieldTrip] Frequency smoothing for beamforming

Yoni Levy yoniilevy at gmail.com
Thu Oct 11 16:55:06 CEST 2012


Hi All,

I am trying to locate a source using beamforming to a short lasting (during
100ms) oscillatory (frequency=28Hz) effect that I find at the sensor level.
The thing is that because of the short time window, the frequency smoothing
is bound to be high, whereas I would like to limit it as much as possible;
not to mention that because trial length varies across subjects and trials,
100ms is the maximal window, but in truth segments are shorter.
Any idea of how I could beamform on such short time window?

Thanks in advance for any ideas,

Yoni



On Fri, Oct 5, 2012 at 12:00 PM, <fieldtrip-request at science.ru.nl> wrote:

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>    1. Re: Frequency smoothing for beamforming (J?rn M. Horschig)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 05 Oct 2012 08:56:27 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Frequency smoothing for beamforming
> Message-ID: <506E849B.7050602 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hey Yoni,
>
> Stephen is right, and just to make this really clear, a Hanning taper
> will always give you a smoothing of your Raleigh frequency (which in
> your case is 3.33Hz). Any taper can only (effectively) smooth in terms
> of your frequency resolution or Raleigh frequency, thus a Hann taper
> gives you the minimal smoothing (apart from a boxcar). Then, the problem
> with different trial becomes more apparent, because since the frequency
> resolution changes, also the smoothing of the Hanning taper changes
> accordingly. I also think that making the trials having equal length is
> the best approach. Having unequal trial lengths also constitutes a
> problem for multitapering, cause you will end up with different tapers
> and different number of tapers per trial. And also your frequency
> smoothing should be a multiple of the Raleigh frequency. You can ask for
> other smoothing, e.g. 8Hz with 3.33Hz resolution, but effectively you
> will see the smoothing at 6.66 or 9.99Hz (depending on where you define
> the end of smoothing) - it's just because you sample in 3.33Hz steps.
> Here you can maybe also see, that having different trial lengths might
> constitute a problem, because you will effectively get different
> smoothing per trial, depending on your Raleigh frequency. The
> computation of the tapers was however correct, so with 8Hz smoothing and
> a 0.3s time window you get 3 tapers ;) Btw, I once played around with it
> and realized that the 3 tapers you obtain are not always the same for
> different parameters, e.g. for 8Hz and 0.25s window you will also get
> 8*0.25*2-1 = 3 tapers, but they will be different from the 3 tapers you
> get with a 0.3s time window. So even that can cause a problem.
>
> Btw, I never heard that different frequency smoothing ends up in
> different part of the brain when beaming. The only reason I can see is
> what Stephen already pointed out, that other frequency bands with
> different functional characteristics smear into your power spectrum.
>
> Best,
> J?rn
>
>
>
>
> On 10/4/2012 3:47 PM, Stephen Whitmarsh wrote:
> > Hi Yoni,
> >
> > Indeed, a simple hanning taper will  already give you a frequency
> > smoothing of +/- 3Hz. Adding tapers can only increase this, and I
> > don't see why you would beamform 22 to 38 Hz if you are interested
> > between in 29-31 Hz. Couldn't you just do cfg.foi = 30, with cfg.taper
> > = 'hanning', giving you a measure of power between of about 27 and 33?
> >
> > You're right that having different trial lenghts will indeed give you
> > a different frequency resolution per trial. If this is a problem is
> > hard to say from here. cfg.minlength = 'maxperlen in ft_redefinetrial
> > would indeed make sure they are all of the same length (i.e. the
> > maximal length) - but if that is different between subjects/conditions
> > that might not be enough.
> >
> > Best,
> > Stephen
> >
> >
> >
> > On 4 October 2012 11:56, Yoni Levy <yoniilevy at gmail.com
> > <mailto:yoniilevy at gmail.com>> wrote:
> >
> >     Hi Stephen!
> >     Thanks for your reply.
> >
> >     My FOI is 29-31Hz; Since my time window is of 300ms, then my freq
> >     smoothing should now be of +/-3.33Hz. If I use a hanning taper,
> >     the parameters that i use for the freqanal (for further on doing
> >     beamformer-statistics) are:
> >             cfg.method ='mtmfft';
> >             cfg.output ='fourier';
> >             cfg.keeptrials = 'yes';
> >             cfg.keeptapers = 'yes';
> >             cfg.taper = 'hanning';
> >             cfg.foilim = [29 31];
> >     However, if I get it right, multitapering should also be an option
> >     as 30Hz is not a relatively very low frequency. In that case, i
> >     remove the hanning and instead include a cfg.tapsmofrq =8, so that
> >     the number of tapers results in 8*0.3*2-1= 3 (I think?). Is it so?
> >
> >     Also, about the time window which is theoretically 300ms, but i
> >     think this depends on the length of every trial; for instance,
> >     before freqanal, when i redefine the trial, i input cfg.minlength
> >     = 'maxperlen'. So if i alter that, the freq smoothing should be
> >     different as well, correct? Ye, anyway, I wonder how to optimize
> >     all those parameters for my source localization statistics.
> >
> >     Thanks in advance,
> >
> >     Yoni
> >
> >
> >     On Wed, Oct 3, 2012 at 3:55 PM, <fieldtrip-request at science.ru.nl
> >     <mailto:fieldtrip-request at science.ru.nl>> wrote:
> >
> >
> >         Hi Yoni!
> >
> >         The extend of the smoothing, I would say, is under normal
> >         circumstances
> >         simply what you
> >         request as a smoothing paramater (given the dpss
> >         characteristics), so I
> >         don't understand
> >         that formulation exactly.
> >
> >         If different smoothings give drastically different result you
> >         might be
> >         sampling
> >         frequencies that behave differently from your frequency of
> >         interest. In
> >         your case, e.g.
> >         perhaps you are adding alpha in your estimate that might
> >         behave differently
> >         in your
> >         paradigm?
> >
> >         I would therefor try to first figure out if your effect is, in
> >         fact,
> >         frequency specific
> >         and try to not to smooth more than necessary to capture that
> >         effect. So
> >         starting with no
> >         (extra) smoothing and looking at the TFR for instance. A
> >         simple FFT would
> >         give you a
> >         frequency smoothing of +/- 1/datalength already (e.g. half a
> >         second would
> >         be +/- 2 Hz).
> >         Simply averaging over frequencies (estimated with a Hanning
> >         taper) instead
> >         of using the
> >         slepian tapers might be a better option.
> >
> >         Then again, you are limited in frequency specificity by the
> >         length of the
> >         data on which
> >         you calculate them. If that is too short you might have
> >         suboptimal and
> >         unexpected
> >         effects. In the case of slepian filters make sure you have at
> >         least a
> >         minimum of 3 tapers
> >         (which is shown in the output of freqanalysis).
> >
> >         There is a lot more to say about tapers, smoothing etc, but I
> >         hope this
> >         helps.
> >
> >         All the best,
> >         Stephen
> >
> >         On 3 October 2012 15:14, Yoni Levy <yoniilevy at gmail.com
> >         <mailto:yoniilevy at gmail.com>> wrote:
> >
> >         > Dear Fieldtrippers,
> >         >
> >         > I am trying to locate the source of an oscillatory effect at
> >         the frequency
> >         > of 30Hz in a time window of interest.
> >         > Before running the ft_sourceanalysis function, I run a
> >         ft_freqanalysis
> >         > with a frequency smoothing of 8 (cfg.tapsmofrq =8).
> >         > My question is whether there is any rule of thumb by which I
> >         could
> >         > reliably determine the extent of the smoothing?
> >         > I found out that even small changes in the 'tapsmofrq' value,
> >         > significantly alter the spatial localization of the
> >         resulting sources.
> >         > For instance, a tapsmofreq value of 8 would point to an
> >         effect in the
> >         > frontal lobe, whereas a value of 10 would point to an effect
> >         in the
> >         > parietal lobe.
> >         >
> >         > Any advice would be appreciated.
> >         >
> >         > Yoni
> >         >
> >
> >
> >     _______________________________________________
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> >     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> >
> >
> >
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>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
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