update: artifact detection

Marcel Bastiaansen Marcel.Bastiaansen at FCDONDERS.RU.NL
Thu Feb 2 17:01:39 CET 2006

Dear Robert,

Thanks for updating the functions. They generally look much better now.
I have a slight problem however. For certain types of analysis (e.g.
multitaper) I need some data before and after the actual trials in my
experiment (to allow tapers to shift into the data at the beginning of
the trial, and out of the data at the end of the trial). Usually I cut
my data so that these extra datapoints are part of the 'trial', but I
don't check these extra datastretches for EOG artefacts (as they fall in
the ITI they typically contain a lot of blinks). I used to do that  by
specifying a negative padding value in the artefact_eog function, but
that is no longer possible. Hence, my question is, whether it would be
possible to include the option of checking only a user-specified part of
each trial for artefacts.
Another thing is that it is not (yet?) possible to call the old artefact
routines in the way you specified it in your message below (though it is
possible to directly call the artefact_eog_old function).


Robert Oostenveld wrote:

> Dear Fieldtrip users,
> I have updated the artifact detection functions (artiact_xxx, where
> xxx=jump, eog and muscle). Each of these three functions was already
> based on the same underlying idea, namely to filter and preprocess
> the data, then z-transform the result, cummulate the z-values over
> channels and finally look for z-values that are larger than the
> cutoff level. To reflect this similarity, I have created a new
> function: artifact_zvalue. Each of the artifact_jump, eog and muscle
> functions now sets some default values and then calls
> artifact_zvalue. That facilitates the maintenance and ensures that
> all functions behave the same regarding graphical feedback. From now
> on, you can also visually verify the trial definition and the
> detected artifacts in rejectartifact, using cfg.artfctdef.feedback=yes.
> Most important for you to know is that:
> 1) the new functions should be largely backward compatible. The
> filtering and preprocessing computations were only marginally
> changed, so the outcome should be almost the same.
> 2) the padding has been better defined. I will also write an artifact
> detection tutorial that explains these padding values better.
> 3) the new artifact detections functions (for jump, eog and muscle)
> now only will work on continuous and pseudo-continuous data. Jumps in
> the data at the trial boundaries for non-continous data are not dealt
> with and will mess up the result so --if you want to use them on
> trial-based data-- you are responsible yourself for configuring the
> padding options correctly.
> 4) the old functions are still available, with the name
> artifact_xxx_old (where xxx=jump, eog and muscle). If you want to use
> them, you should specify cfg.artifact.type={'eog_old', ...} and call
> the rejectartifact function.
> The idea (which I will describe in the upcoming "artifact tutorial")
> is that you do not use cfg.rejectjump/muscle/eog=yes any more in the
> preprocessing cfg structure, but that you do the following steps
> seperately:
>   cfg = something to start with...
>   cfg = definetrial(cfg)
>   cfg = artifact_eog(cfg)
>   cfg = artifact_eog(cfg)
>   cfg = artifact_jump(cfg)
>   cfg = artifact_muscle(cfg)
>   cfg = rejectartifact(cfg)
>   data = preprocessing(cfg)
> The fieldtrip version on home/common (inside the FCDC) will be
> updated this afternoon. The fieldtrip version on the ftp server
> (outside the FCDC) will be updated this evening.
> Since it is a large change in the fieldtrip code, bugs might have
> crept in. Please be extra cautious the upcoming time and report
> unusual behaviour. Sorry for the inconvenience that this may result in.
> best regards,
> Robert
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Robert Oostenveld, PhD
> F.C. Donders Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> phone: +31-24-3619695
> http://www.ru.nl/fcdonders/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

dr. Marcel C.M. Bastiaansen.
FC Donders Centre for Cognitive Neuroimaging
Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands
Mailing address: Trigon 181, PO Box 9101, 6500 HB Nijmegen, the Netherlands
phone: + 31 24 3610 882
fax:   + 31 24 3610 989
mail: marcel.bastiaansen at fcdonders.ru.nl

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