[FieldTrip] automatic artifact detection and ft_denoise_pca

[Stephen Whitmarsh]

Dear Robin,

Please allow me to refer you to the excellent documentation on (negative)
padding and artifact rejection in this gorgeous didactical masterpiece, a
joy to behold:
***** http://fieldtrip.fcdonders.nl/tutorial/automatic_artifact_rejection*****

;-)
Stephen

On 6 February 2013 15:07, Robin <robince at gmail.com> wrote:

> Hi Jörn,
>
> Thanks very much. Yes I think that will solve the problem - I hadn't
> realised I could use negative trial padding values.
> What I had just got working was as similar approach extracting larger
> trials at first and then manually making a new trl defintion:
>
>     % artifact detection
>     tmpcfg = [];
>     tmpcfg.continuous = 'no'; % some trials are excluded
>     tmpcfg.trl = run_clean.sampleinfo;
>     tmpcfg.trl(:,1) = tmpcfg.trl(:,1) + round(filterpad*run_clean.fsample);
>     tmpcfg.trl(:,2) = tmpcfg.trl(:,2) - round(filterpad*run_clean.fsample);
>
>     [tmpcfg, artifact] = ft_artifact_muscle(tmpcfg, run_clean);
>
> which seemed to work but the trlpadding option definitely looks cleaner!
>
> Thanks,
>
> Robin
>
> On Wed, Feb 6, 2013 at 2:02 PM, "Jörn M. Horschig"
> <jm.horschig at donders.ru.nl> wrote:
> > Hi Robin,
> >
> > I think the steps you suggested sound reasonable, but I do not see how
> you
> > are avoiding the filter artifact issue there, you just postpone it to a
> > later stage. Instead it might be a smart way to 'pad' your trials when
> > defining them with 1s pre- and post (so cut out more than you need); that
> > way all filter artifacts will be in that 1s that you are not interested
> in
> > anyway. Then, you can define cfg.xxx.trlpadding =-1 prior to calling
> > ft_artifact_xxx (thereby ignoring that 1s of  'padded' data). If I
> > understand your question correctly, that solves your problem, doesn't it?
> >
> > Best,
> > Jörn
> >
> >
> >
> > On 2/6/2013 12:54 PM, Robin wrote:
> >>
> >> Hi all,
> >>
> >> I am a new fieldtrip user getting started preprocessing a large MEG
> >> data set (I am in Glasgow and the data was collected at CCNi).
> >>
> >> I think I am slowly getting to grips with all the steps necessary, but
> >> I have a question about the artifact rejection.
> >>
> >> My undersanding is that the denoise procedure helps correct external
> >> sources of noise, so having the signal cleaned in this way should help
> >> detect the biological artifacts which are valid magnetic signal at the
> >> scalp. But I can't see an easy way to do this since the ft_artifact_*
> >> functions want to load the raw continuous data from disk. I can get
> >> them to act on the in memory trials data if I set the padding options
> >> to 0, but then I get an unacceptable amount of rejections (I guess
> >> because of the filter artifacts the padding usually prevents).
> >>
> >> Is it possible to run ft_artifact_muscle, ft_artifact_eog etc. on the
> >> denoised signal from ft_denoise_pca and if so how?
> >>
> >> At the moment I am performing the following steps:
> >>
> >> Load each run
> >> Detect jumps with ft_artifact_jump.
> >> Concatenate the jump-free trials from all runs together for this block.
> >>
> >> Visually inspect the reference channels and remove high variance
> >> trials (across the whole block).
> >> Compute denoise PCA weights using only good reference data (and no MEG
> >> jump) trials across the whole block.
> >>
> >> I would now like to apply the denoise PCA weights, perform other
> >> automatic artifact removal on the cleaned data, before further visual
> >> inspection and the next steps of ICA etc.
> >>
> >> Is there any problems with this strategy?
> >>
> >> Thanks in advance for any advice,
> >>
> >> Robin
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >
> > --
> > Jörn M. Horschig
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen
> > Neuronal Oscillations Group
> > FieldTrip Development Team
> >
> > P.O. Box 9101
> > NL-6500 HB Nijmegen
> > The Netherlands
> >
> > Contact:
> > E-Mail: jm.horschig at donders.ru.nl
> > Tel:    +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> >
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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