[FieldTrip] modification in newest version ft_redefinetrial

[Andreas Wollbrink]

Hi Jan Mathijs,

thanks a lot you for your insightful comments.
You have 'hit the nail on the head' (as we say in German).
There was indeed a certain misunderstanding about the different meaning
of the parameter 'continuous' in the Fieldtrip functions mentioned.

Thank you very much for the help!

Best,
Andreas

On Wed, 2021-09-22 at 14:54 +0000, Schoffelen, J.M. (Jan Mathijs) via
fieldtrip wrote:
> Dear Andreas,
> 
> This is truly a lightspeed pick up of some new functionality that
> only came available this morning!
> 
> I think that there may be some confusion w.r.t. the meaning of the
> option ‘continuous’ in ft_preprocessing vs. ft_redefinetrial, and
> perhaps also with respect to when to use ft_definetrial or
> ft_redefinetrial.
> 
> Clearly, ft_definetrial is intended to decorate the input cfg
> structure with a ’trl’ field, which is the recipe for the epochs.
> 
> cfg.continuous is an option for ft_preprocessing to be able to deal
> with CTF’s ‘pseudocontinuous’ recording mode, which essentially means
> that every 10 seconds or so (in a continuous data stream) a ’trial’
> trigger is inserted in the data, which caused the original reading
> functions to choke if samples across these artificial boundaries were
> detected. 
> 
> on the other hand, cfg.continuous in ft_redefinetrial has a different
> meaning and functionality. It is intended as a recipe to ’stitch back
> together’ chunks of data, that before for some reason became
> unstitched. There are not many exotic use cases that would need this,
> and it is even dangerous to apply this option too enthusiastically,
> but the typical use case would be something like this:
> 
> cfg = [];
> cfg = <somedataset>
> data = ft_preprocessing(cfg); %->reads in the data as a very long
> chunk
> 
> cfg = [];
> cfg.length = 2;
> data = ft_redefinetrial(cfg, data); %-> chops up the data in 1 s
> snippets
> 
> cfg = [];
> cfg.method = ’summary’;
> cfg.keeptrial = ’nan’;
> data = ft_rejectvisual(cfg, data); %-> results in chunked data with
> ‘artifiacts’ nanned out
> 
> cfg = [];
> cfg.continuous = ‘yes’;
> data = ft_redefinetrial(cfg, data); %-> stitches everything back
> together again, but now with NaNs at the one-second windows
> containing artifacts
> 
> As an important side note: This is risky once you start filtering the
> individual chunks before you stitch them together again, because you
> introduce boundary effects, which were not there 
> initially.
> 
> 
> Using cfg.trl in ft_redefinetrial, where the input data typically
> contains one (or a few) very long segments of data should not require
> the cfg.continuous option to be specified, not even if this was
> needed for ft_preprocessing in the first place. My suspicion is that
> you stumbled across this because of what I just said, so the solution
> to your problem is to start from an empty cfg before calling
> ft_redefinetrial (and not recycle the one you also used for
> ft_preprocessing).
> Please let me know if I totally ‘missed the plank’, as we’d say in
> Dutch.
> 
> Best wisehs,
> JM
> 
> 
> 
> 
> 
> 
> > On 22 Sep 2021, at 15:55, Andreas Wollbrink via fieldtrip <
> > fieldtrip at science.ru.nl> wrote:
> > 
> > Dear Fieldtrip community,
> > 
> > my question is probably more directed to the Fieldtrip developers,
> > but
> > should be of interest to the rest of the users as well.
> > I just noticed that in the latest Fieldtrip version (revision
> > 0cafbf72b) in the function ft_redefinetrial in line 156 there are
> > some
> > plausibility queries that exclude the mutual presence of cfg.trl
> > and
> > cfg.continuous. 
> > Can't this make sense if cfg.trl is obtained from a previous call
> > to
> > ft_definetrial and the data itself was recorded continuously?
> > What is the recommendation then on how to call the ft_redefinetrial
> > function?
> > 
> > Thanks a lot for the help.
> > 
> > Best, Andreas
> > 
> > -- 
> > Andreas Wollbrink, 
> > Dipl.-Ing., Biomedical Engineer
> > 
> > MEG / EEG Lab Manager
> > 
> > Institute for Biomagnetism and Biosignalanalysis
> > University Hospital, University of Muenster
> > 
> > Malmedyweg 15, 48149 Muenster, Germany
> > 
> > office:    +49-251-83-52546
> > email: a.wollbrink at wwu.de
> > 
> > https://urldefense.com/v3/__http://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/andreas-wollbrink__;!!HJOPV4FYYWzcc1jazlU!pjFq8SOuM1EcP-viSP-nhi5lt4TLaOCmAUl1HEjHVL4ssvU8EBe0uhO5IVxTK5ayqoDhyxMFREo5cf8$ 
> > 
> > 
> > 
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-- 
Andreas Wollbrink, 
Dipl.-Ing., Biomedical Engineer

MEG / EEG Lab Manager

Institute for Biomagnetism and Biosignalanalysis
University Hospital, University of Muenster

Malmedyweg 15, 48149 Muenster, Germany

office:    +49-251-83-52546
email: a.wollbrink at wwu.de

http://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/andreas-wollbrink