using reference gradiometers with preproc_denoise

[jan-mathijs schoffelen]

Dear Mark,

Adding this functionality to the fieldtrip release is on my to do
list. I'll let you know when it's there.

Best,

JM

On Nov 5, 2010, at 10:15 AM, Mark Drakesmith wrote:

> 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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>>> You are receiving this message because you are subscribed to
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>>> discussion
>>> 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.
>>> ---------------------------------------------------------------------------
>>>
>>
>> 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
>>
>> ---------------------------------------------------------------------------
>> You are receiving this message because you are subscribed to
>> the  FieldTrip list. The aim of this list is to facilitate the
>> discussion
>> 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.
>> ---------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the
> discussion
> 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.
> ---------------------------------------------------------------------------
>

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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You are receiving this message because you are subscribed to
the  FieldTrip list. The aim of this list is to facilitate the discussion
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.
---------------------------------------------------------------------------