[FieldTrip] Problems with automatic artifact rejection

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Mon Oct 24 13:29:02 CEST 2011


Hi Alicia,

OK. Good that you found the solution. This indicates to me that you have been using an older version of FieldTrip, where the option indeed was called 'feedback'. In the newer FieldTrip version, this option has been renamed into 'interactive'. We try to provide backward compatibility support, so in general a newer version still works (for a while at least) with old options. The other way around is of course not possible to achieve in general. In this case the documentation was up-to-date, but your code was not. I would expect the problem to go away if you download a recent version of FieldTrip.

Best wishes,

Jan-Mathijs


On Oct 24, 2011, at 1:13 PM, Alicia González wrote:

> Hi,
> 
> I solved the problem adding:
>  cfg.artfctdef.zvalue.feedback = 'yes';
> Now I can see the figures of the z-score of the processed data. 
> 
> El 21 de octubre de 2011 11:08, Alicia González <ali.gm88 at gmail.com> escribió:
> I'm using the data provided in the tutorial: ArtifactMEG.ds (This dataset was acquired continuously with trials of 10 seconds, and during the recording the experimenter instructed the subject to make artifacts and wrote down the trial number in which the artifacts were made)
> And I running the code below:
> 
> cfg                    = [];
> cfg.dataset            = 'ArtifactMEG.ds';
> cfg.headerformat       = 'ctf_ds';
> ctf.dataformat         = 'ctf_ds'; 
> cfg.trialdef.eventtype = 'trial';
> cfg                    = ft_definetrial(cfg);
> 
> trl                    = cfg.trl(1:50,:); % just use the first 50 trials for the time being
> 
> % jump
> cfg                    = [];
> cfg.trl = trl;
> cfg.padding = 0;
> cfg.datafile   = 'ArtifactMEG.ds';
> cfg.headerfile = 'ArtifactMEG.ds';
> cfg.continuous = 'yes';
>  
> % channel selection, cutoff and padding
> cfg.artfctdef.zvalue.channel    = 'MEG';
> cfg.artfctdef.zvalue.cutoff     = 20;
> cfg.artfctdef.zvalue.trlpadding = 0.5*cfg.padding;
> cfg.artfctdef.zvalue.artpadding = 0.5*cfg.padding;
> cfg.artfctdef.zvalue.fltpadding = 0;
>  
> % algorithmic parameters
> cfg.artfctdef.zvalue.cumulative    = 'yes';
> cfg.artfctdef.zvalue.medianfilter  = 'yes';
> cfg.artfctdef.zvalue.medianfiltord = 9;
> cfg.artfctdef.zvalue.absdiff       = 'yes';
>  
> % make the process interactive
> cfg.artfctdef.zvalue.interactive = 'yes';
>  
> [cfg, artifact_jump] = ft_artifact_zvalue(cfg);
> 
> 2011/10/21 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> Hi Alicia,
> 
> In order to be able to address your problem we need some additional feedback of course. What kind of data are you using, etc?
> 
> BW, 
> 
> JM
> 
> On Oct 21, 2011, at 8:34 AM, Alicia González wrote:
> 
>> 
>> 
>> Hi, 
>> 
>> I'm trying to do automatic artifact rejection using the tutorial on the site. It seems that everything runs ok but, when I try to see the z-score figure setting cfg.artfctdef.zvalue.interactive = 'yes', nothing appears (and no errors are found). I'm just using the code from the tutorial without changes.
>> 
>> thanks in advance.
>> 
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> Jan-Mathijs Schoffelen, MD PhD 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
> 
> 
> _______________________________________________
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> 
> 
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Jan-Mathijs Schoffelen, MD PhD 
Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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