[FieldTrip] automatic artifact detection and ft_denoise_pca
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Wed Feb 6 15:38:59 CET 2013
only a brilliant mind might have created such a guide - chapeau ^^
On 2/6/2013 3:17 PM, Stephen Whitmarsh wrote:
> 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
> <mailto: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 <mailto: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 <mailto: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 <mailto:jm.horschig at donders.ru.nl>
> > Tel: +31-(0)24-36-68493 <tel:%2B31-%280%2924-36-68493>
> > 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 <mailto:fieldtrip at donders.ru.nl>
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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>
>
>
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--
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
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