[FieldTrip] automatic artifact detection and ft_denoise_pca

[Robin]

Hi Stephen,

Thanks very much - I think I get it now. Combined with a
f_redefinetrial at the end to cut back just the bit I want it seems to
work well.

In fact it is working so well that almost all my trials are rejected
:) but I think that is another problem!

Cheers

Robin

On Wed, Feb 6, 2013 at 2:17 PM, Stephen Whitmarsh
<stephen.whitmarsh at gmail.com> 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> 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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