[FieldTrip] more on artfifact rejection

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Mon Jan 24 16:41:09 CET 2011


Hmmm, apparently this approach needs to be ironed out a bit (also from  
our side). For now, I'd say that it should work if you keep per type  
of artifact the  artifact field in the output configuration, and just  
concatenate these prior to calling ft_rejectartifact. I will moreover  
CC this e-mail to the people involved in creating the first version of  
the renewed tutorial, and will bring up the issue in this week's  
FieldTrip developers meeting.

Best,

JM

On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote:

> 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
> <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





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