[FieldTrip] ft_denoise_synthetic 3rd order grad

[Barbara Haendel]

Hey there, thanks a lot for the replies!

Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. 

Thanks again,
Barbara




-------- Original-Nachricht --------
> Datum: Mon, 16 Apr 2012 17:53:56 +0200
> Von: Panagiotis Tsiatsis <Panagiotis.Tsiatsis at Tuebingen.MPG.de>
> An: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>
> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad

> Hello girls and guys,
> 
> It is working for my CTF MEG data - the version that I have is v4692 
> 2011-11-07.
> 
> The other thing that might cause a problem could be ommiting the 
> reference channels definition before the ft_ preprocessing command that 
> gave you your "dataprepro"
> 
> i.e maybe you might  need something like this
> 
> cfg = [];
> 
> ...
> //various preprocessing parameters
> ...
> 
> cfg.channel            = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'};
> 
> dataprepro = ft_preprocessing(cfg);
> 
> 
> Hope you are lucky :)
> 
> Best,
> Panagiotis
> 
> 
> On 4/16/2012 4:59 PM, Stan van Pelt wrote:
> > Hi Barbara,
> >
> > I can replicate your finding, but am unsure what is causing it. Maybe 
> > the difference/correction is lower than the Matlab or CTF precision? 
> > In any case, if the 3rd order gradients were on, ft_denoise_synthetic 
> > would undo the G3BR-balancing, ergo it toggles.
> >
> > Best,
> > Stan
> >
> >
> > ------------------------------------------------------------------------
> >
> >     *Van: *"Michael Wibral" <michael.wibral at web.de>
> >     *Aan: *"Email discussion list for the FieldTrip project"
> >     <fieldtrip at donders.ru.nl>
> >     *Verzonden: *Maandag 16 april 2012 16:46:27
> >     *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad
> >
> >     Hi Barbara,
> >
> >     are you certain that the original data do not have 3rd gradients
> >     enabled? - looking at them once in dataEditor, switching to 3rd
> >     grads and accidentally forgetting to unclick 'save parameters with
> >     dataset' will make them have 3rd grads...
> >
> >     When I last used ft_denoise_synthetic it worked pretty much as
> >     described (??).
> >
> >     Michael
> >
> >     *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr
> >     *Von:* "Barbara Haendel" <B.Haendel at gmx.net>
> >     *An:* fieldtrip at donders.ru.nl
> >     *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad
> >
> >     Dear fieldtrip users,
> >
> >     has anyone experience in using ft_denoise_synthetic? If I try to
> >     calculate 3rd order grads in the below specified way the data does
> >     not change with respect to the input data (which has no synthetic
> >     gradiometer applied). Is there some obvious misunderstanding on my
> >     side of how to use this function or is our environment truly
> >     noiseless :)
> >
> >     Cheers,
> >     Barbara
> >
> >     cfg=[];
> >     cfg.gradient ='G3BR';
> >     cfg.trials = 'all';
> >     data_3rdorder = ft_denoise_synthetic(cfg, dataprepro);
> >
> >
> >     >> data_3rdorder.grad.balance
> >
> >     ans =
> >
> >     G1BR: [1x1 struct]
> >     G2BR: [1x1 struct]
> >     G3BR: [1x1 struct]
> >     current: 'G3BR'
> >     previous: {'none'}
> >
> >     >> sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:))
> >
> >     ans = 0
> >
> >     -- 
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> >
> >
> >     _______________________________________________
> >     fieldtrip mailing list
> >     fieldtrip at donders.ru.nl
> >     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >
> >
> > -- 
> > Stan van Pelt
> >
> > Donders Institute for Brain, Cognition and Behaviour, Radboud 
> > University Nijmegen
> > Kapittelweg 29, 6525 EN Nijmegen, Netherlands
> > E-mail:  stan.vanpelt at donders.ru.nl
> > Website: www.ru.nl/donders/
> > Phone:  (+31) (0)24 36 10981
> > Fax:    (+31) (0)24 36 10989
> >
> >
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> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> -- 
> Panagiotis S. Tsiatsis
> Max Planck Institute for Biological Cybernetics
> Cognitive NeuroImaging Group
> Tuebingen, Germany
> 

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