update: artifact detection

Dr. Jose Luis Patino Vilchis luis.patino at UNIKLINIK-FREIBURG.DE
Fri Feb 3 08:44:53 CET 2006


Dear Robert,

Is it there a paper explaining how the muscle artifact rejection is done?

best regards

Luis Patino


Zitat von Marcel Bastiaansen <Marcel.Bastiaansen at fcdonders.ru.nl>:

> 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).
>
> Best,
> Marcel
>
>
> 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
> web:
>
http://www.ru.nl/aspx/get.aspx?xdl=/views/run/xdl/page&ItmIdt=20592&SitIdt=119&VarIdt=96
> --
>
>



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