[FieldTrip] ft_denoise_synthetic 3rd order grad

[jan-mathijs schoffelen]

Hi Barbara,

Good plan to adjust the code a bit in this respect. Could you please file a bug about this on our bugzilla list: bugzilla.fcdonders.nl

Best wishes,

Jan-Mathijs


On Apr 19, 2012, at 8:59 AM, Barbara Haendel wrote:

> 
> 
> 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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>>> 
>>>    _______________________________________________
>>>    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
>>> 
>>> 
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
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>> 
>> 
>> -- 
>> Panagiotis S. Tsiatsis
>> Max Planck Institute for Biological Cybernetics
>> Cognitive NeuroImaging Group
>> Tuebingen, Germany
>> 
> 
> -- 
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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