[FieldTrip] ft_denoise_synthetic 3rd order grad

[Panagiotis Tsiatsis]

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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>
>
>
> -- 
> 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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-- 
Panagiotis S. Tsiatsis
Max Planck Institute for Biological Cybernetics
Cognitive NeuroImaging Group
Tuebingen, Germany

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