[FieldTrip] more on artfifact rejection

Michael Wibral michael.wibral at web.de
Mon Jan 24 13:51:38 CET 2011


Hi Jan mathijs,

I tried to get option1 running, stumbled over the following little obstacle however:

I tried to keep one cfg throughout the steps ft_definetrial; ft_artifact_zvalue, ft_rejectartifcat (with option complete and some tracking of where artfecats were found), ft_preprocessing (cutting out the clean trials from the cont. data). IMHO this used to be the way most people did this kind of procesing a while ago.

However, I can't get ft_artifact_zvalue to run with different settings one after another for jump/musvle/EOG. FT claims after the first run of ft_artifact_zvalue that the z-value thing has been performed and refuse to detect other artifacts with new settings.

>From here I only see two alternative: specifying a really lengthy cfg every time a new (also struggling with the cfg.dataset versus cfg.datafile issue) and do the bookkeeping of cfg.trl and related things myself or manually removing the cfg.artdef.zvalue.artifct field to get the z-value based detection to run again. This seems a bit odd to me.

Any suggestions?

Michael




-----Urspr√ľngliche Nachricht-----
Von: "jan-mathijs schoffelen" <jan.schoffelen at donders.ru.nl>
Gesendet: Jan 24, 2011 12:12:57 PM
An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
Betreff: Re: [FieldTrip] more on artfifact rejection

>Dear Michael,
>
>I agree. The tutorial should be 'de'-confused by sketching option 1,  
>and another one should be describing option 2, or the original should  
>be clearly making the distinction.
>
>Best,
>
>JM
>
>
>On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote:
>
>> Hi Jan-Mathijs,
>>
>> I am a bit unsure how to proceed:
>>
>> (1) sketch the artifact correction way like this
>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact ->  
>> ft_preprocessing
>> OR
>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) ->  
>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing.
>>
>> I think I should go for option (1) as this seems to be the standard  
>> use on continuous data. Sometime in the futrure one should then add  
>> a tutorial for those that have data in trials to start with.
>>
>> Michael
>>
>> -----Urspr√ľngliche Nachricht-----
>> Von: "jan-mathijs schoffelen" <jan.schoffelen at donders.ru.nl>
>> Gesendet: Jan 21, 2011 9:55:48 AM
>> An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl 
>> >
>> Betreff: Re: [FieldTrip] more on artfifact rejection
>>
>>> Dear Michael,
>>>
>>> Yes, I agree with you here as well. In principle the
>>> ft_artifact_zvalue supports data as a second input argument, but in
>>> such case the different types of padding in the cfg do not make  
>>> sense.
>>> I would indeed remove the second input arguments in the example code
>>> snippets. Could I ask you to take care of that?
>>>
>>> Thanks,
>>>
>>> JM
>>>
>>>
>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote:
>>>
>>>> Deal Fieldtrip users,
>>>>
>>>> there is something else I do not understand in the tutorial: if you
>>>> read in the data in trials (as it is done) how can you do padding
>>>> later as it is suggested. I tried to run the example code on teh
>>>> website  reading in the data such that it contains trials. If I then
>>>> try to search for muscle artifacts I get the 'subscript indices must
>>>> be positive or logical ... values', indicating that the code tries
>>>> to access data that aren't there. If I set the padding to zero
>>>> (instead of 0.1) it works. So I am wondering wether somehow one
>>>> should actually run these things on continuous data (contrary to
>>>> what is indicated in the tutorial)?
>>>>
>>>> Michael
>>>> <Michael Wibral.vcf><Michael
>>>> Wibral.vcf>_______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>> Dr. J.M. (Jan-Mathijs) Schoffelen
>>> Donders Institute for Brain, Cognition and Behaviour,
>>> Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>> J.Schoffelen at donders.ru.nl
>>> Telephone: 0031-24-3614793
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> <Michael Wibral.vcf>_______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>Dr. J.M. (Jan-Mathijs) Schoffelen
>Donders Institute for Brain, Cognition and Behaviour,
>Centre for Cognitive Neuroimaging,
>Radboud University Nijmegen, The Netherlands
>J.Schoffelen at donders.ru.nl
>Telephone: 0031-24-3614793
>
>
>_______________________________________________
>fieldtrip mailing list
>fieldtrip at donders.ru.nl
>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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