[FieldTrip] ft_denoise_synthetic 3rd order grad

Tue Apr 24 10:26:18 CEST 2012

Hi Stan,

To me, it seems all three options would be fine, and I actually don't
think they are computationally suboptimal. I would probably go for
option 2, and have done so with a similar problem in the past. This
worked well for me.

Best,
Eelke

On 24 April 2012 10:14, Stan van Pelt <stan.vanpelt at fcdonders.ru.nl> wrote:
> Hi all,
>
> A follow-up question on the implementation of 3rd-order gradiometer
> correction in FT:
>
> I am puzzling how one can do both 3-order grad. correction and dft-filtering
> properly using FT. the logical sequency would be to do ft_denoise_synthetic
> first, and subsequently dft-filtering using ft_preprocessing. However, in
> that case it is no longer possible to pad the data when calling
> ft_preprocessing, because it now processes trial-data (output from
> ft_denoise_synthetic), and doesn't read in the original dataset anymore. or
> am I mistaken here?
>
> I could see 3 alternatives, which seem to be more
> like (computationally) suboptimal workarounds:
> - Apply ft_denoise_synthetic on the entire dataset, then dft-filter the
> entire dataset, and then run ft_redefinetrial to cut the data into actual
> trials
> - Adjust the trial definition such that longer data segments are read in,
> equivalent to your padding size. Then apply ft_denoise_synthetic on these
> trials, then dft-filter them, and then run ft_redefinetrial to cut the data
> into actual trials
> - Doing the 3-rd order grad. correction first using the DataEditor, and then
> process it further using FT.
>
> Any thoughts?
>
> Best, Stan
>
>
> ________________________________
>
> Van: "Michael Wibral" <michael.wibral at web.de>
> Aan: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> Verzonden: Donderdag 19 april 2012 10:24:57
> Onderwerp: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad
>
>
> Hey there,
>
> sorry for not thinking about it any earlier, indeed I can confirm that
> ft_denoise.. needs the reference channels to function properly. I remember
> having to preprocess in a funny order in old ft versions, to do artefcat
> rejection without the refs and denoising with the refs.
>
> Personally, I think the code should check whether the refs are there and
> otherwise throw an error. Since ft_denoise.. only concerns CTF (and bti??)
> systems, where the refs have fixed names this could be easily implemented,
> or am I mistaken?
>
> Best,
> Michael
> Gesendet: Donnerstag, 19. April 2012 um 08:59 Uhr
> Von: "Barbara Haendel" <B.Haendel at gmx.net>
> An: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>, fieldtrip at donders.ru.nl
> Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad
>
>
> 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
>> >
>> > --
>> > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!
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>> >
>> >
>> > _______________________________________________
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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
>> >
>> >
>> > _______________________________________________
>> > fieldtrip mailing list
>> > 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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>
>
>
> _______________________________________________
> 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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