Dear Robin,<div><br></div><div>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: </div><div>***** <a href="http://fieldtrip.fcdonders.nl/tutorial/automatic_artifact_rejection">http://fieldtrip.fcdonders.nl/tutorial/automatic_artifact_rejection</a> *****</div>
<div><br></div><div>;-)</div><div>Stephen<br><br><div class="gmail_quote">On 6 February 2013 15:07, Robin <span dir="ltr"><<a href="mailto:robince@gmail.com" target="_blank">robince@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jörn,<br>
<br>
Thanks very much. Yes I think that will solve the problem - I hadn't<br>
realised I could use negative trial padding values.<br>
What I had just got working was as similar approach extracting larger<br>
trials at first and then manually making a new trl defintion:<br>
<br>
% artifact detection<br>
tmpcfg = [];<br>
tmpcfg.continuous = 'no'; % some trials are excluded<br>
tmpcfg.trl = run_clean.sampleinfo;<br>
tmpcfg.trl(:,1) = tmpcfg.trl(:,1) + round(filterpad*run_clean.fsample);<br>
tmpcfg.trl(:,2) = tmpcfg.trl(:,2) - round(filterpad*run_clean.fsample);<br>
<br>
[tmpcfg, artifact] = ft_artifact_muscle(tmpcfg, run_clean);<br>
<br>
which seemed to work but the trlpadding option definitely looks cleaner!<br>
<br>
Thanks,<br>
<br>
Robin<br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, Feb 6, 2013 at 2:02 PM, "Jörn M. Horschig"<br>
<<a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>> wrote:<br>
> Hi Robin,<br>
><br>
> I think the steps you suggested sound reasonable, but I do not see how you<br>
> are avoiding the filter artifact issue there, you just postpone it to a<br>
> later stage. Instead it might be a smart way to 'pad' your trials when<br>
> defining them with 1s pre- and post (so cut out more than you need); that<br>
> way all filter artifacts will be in that 1s that you are not interested in<br>
> anyway. Then, you can define cfg.xxx.trlpadding =-1 prior to calling<br>
> ft_artifact_xxx (thereby ignoring that 1s of 'padded' data). If I<br>
> understand your question correctly, that solves your problem, doesn't it?<br>
><br>
> Best,<br>
> Jörn<br>
><br>
><br>
><br>
> On 2/6/2013 12:54 PM, Robin wrote:<br>
>><br>
>> Hi all,<br>
>><br>
>> I am a new fieldtrip user getting started preprocessing a large MEG<br>
>> data set (I am in Glasgow and the data was collected at CCNi).<br>
>><br>
>> I think I am slowly getting to grips with all the steps necessary, but<br>
>> I have a question about the artifact rejection.<br>
>><br>
>> My undersanding is that the denoise procedure helps correct external<br>
>> sources of noise, so having the signal cleaned in this way should help<br>
>> detect the biological artifacts which are valid magnetic signal at the<br>
>> scalp. But I can't see an easy way to do this since the ft_artifact_*<br>
>> functions want to load the raw continuous data from disk. I can get<br>
>> them to act on the in memory trials data if I set the padding options<br>
>> to 0, but then I get an unacceptable amount of rejections (I guess<br>
>> because of the filter artifacts the padding usually prevents).<br>
>><br>
>> Is it possible to run ft_artifact_muscle, ft_artifact_eog etc. on the<br>
>> denoised signal from ft_denoise_pca and if so how?<br>
>><br>
>> At the moment I am performing the following steps:<br>
>><br>
>> Load each run<br>
>> Detect jumps with ft_artifact_jump.<br>
>> Concatenate the jump-free trials from all runs together for this block.<br>
>><br>
>> Visually inspect the reference channels and remove high variance<br>
>> trials (across the whole block).<br>
>> Compute denoise PCA weights using only good reference data (and no MEG<br>
>> jump) trials across the whole block.<br>
>><br>
>> I would now like to apply the denoise PCA weights, perform other<br>
>> automatic artifact removal on the cleaned data, before further visual<br>
>> inspection and the next steps of ICA etc.<br>
>><br>
>> Is there any problems with this strategy?<br>
>><br>
>> Thanks in advance for any advice,<br>
>><br>
>> Robin<br>
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><br>
><br>
><br>
> --<br>
> Jörn M. Horschig<br>
> PhD Student<br>
> Donders Institute for Brain, Cognition and Behaviour<br>
> Centre for Cognitive Neuroimaging<br>
> Radboud University Nijmegen<br>
> Neuronal Oscillations Group<br>
> FieldTrip Development Team<br>
><br>
> P.O. Box 9101<br>
> NL-6500 HB Nijmegen<br>
> The Netherlands<br>
><br>
> Contact:<br>
> E-Mail: <a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><br>
> Tel: <a href="tel:%2B31-%280%2924-36-68493" value="+31243668493">+31-(0)24-36-68493</a><br>
> Web: <a href="http://www.ru.nl/donders" target="_blank">http://www.ru.nl/donders</a><br>
><br>
> Visiting address:<br>
> Trigon, room 2.30<br>
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><br>
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</div></div></blockquote></div><br></div>