using reference gradiometers with preproc_denoise

[Mark Drakesmith]

Thanks for the clarification. That's very helpful. I was not aware of the cfw and afw commands. Would it be possible to obtain the matlab scripts? Our 4d machine is now out of service so accessing the 4d software may be difficult. 
 
Thanks again

Mark Drakesmith


On 5 Nov 2010, at 08:20, jan-mathijs schoffelen <jan.schoffelen at DONDERS.RU.NL> wrote:

> Dear Mark,
> 
> preproc_denoise has been specifically designed to remove the very high amplitude coil signals generated by the 4D system when continuous head localization is switched on. It is regressing out the signals on the reference coils on a trial by trial basis. The signal to noise of this artifact is huge (in fact, you don't see any brain signal when the coils are switched on), and as a consequence of this the regression coefficients are relatively stable across trials. In order to remove lower amplitude environmental noise, a single trial estimate of the regression coefficients is probably not what you want. The 4D-software comes with the command line utitilties cfw and afw, which computes a set of balancing coefficients given some input data (typically across a whole dataset). Did you try to use this? I have a matlab implementation which achieves the same thing, but it is not yet part of general FieldTrip.
> 
> Best,
> 
> Jan-Mathijs
> 
> 
> On Nov 4, 2010, at 7:11 PM, Mark Drakesmith wrote:
> 
>> Hi
>> 
>> I am just looking over some MEG data and was wondering what is the best way of dealing with noise. the 4D MEG scanner includes 11 reference coils for detecting noise within the MSR. What is the best way of using this for data-cleaning? I am currently using preproc_denoise to do this, but the description suggests it should be used when continuous head motion channels are used, which is not the case here. Is it appropriate to use preproc_denoise or should I be using an ICA-type approach?
>> 
>> Any help clearing up this confusion would be greatly appreciated.
>> 
>> Regards
>> 
>> Mark
>> 
>> -- 
>> 
>> Mark Drakesmith
>> PhD Student
>> 
>> Neuroscience and Aphasia Research Unit (NARU)
>> University of Manchester
>> 
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> 
> 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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> between  users of the FieldTrip  toolbox, to share experiences
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> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
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You are receiving this message because you are subscribed to
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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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