Beamformer time course
Marie Smith
marie at PSY.GLA.AC.UK
Wed May 24 19:27:06 CEST 2006
Hi,
Thanks for the pointer to the earlier discussion, unfortunately it
does not answer my question.
I had assumed that the dics filters were output for a fixed dipole
orientation (that which maximizes filter output) - hence i was
expecting to have a 1 dimensional set of filter weights with which to
compute a time series (cf. a virtual channel).
I am unsure how to interpret the three time series resulting from
multiplying the 3D filter with the time series. Does this mean the
orientation could change trial per trial and time point per time point?
Does this mean that for calculations involving the time course (e.g.
synchrony) that you only use the amplitude, disregarding the
orientation?
Thanks,
Marie
On 24 May 2006, at 08:25, Jan Mathijs Schoffelen wrote:
> Dear Marie,
>
> Please have a look in the discussion's list archive. A question
> very similar
> to yours has been answered: see the archive of May 2006, and follow
> the link
> "source reconstruction". The discussion's list archive can be
> reached from
> the website.
>
>
> Yours,
>
> Jan-Mathijs
>
> The dimensionality of the filter is a 3xN-matrix, with N the number of
> sensors. The "3" corresponds with the x,y,z direction in space. In
> other
> words: multiplying your data with the filter results in a 3xT
> (number of
> time points) matrix, which represents a dipole's activity in 3-D
> space.
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On Behalf
> Of Marie Smith
> Sent: Tuesday, May 23, 2006 7:47 PM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] Beamformer time course
>
> Hi,
>
> Thanks again for all your help with my questions so far, it has been
> very useful.
>
> As an alternative method to determining the time course of
> activation, I planned to use the filter as output from sourceanalysis
> directly with the time locked data set.
> However I am unsure what the three dimensions of the filter are.
> Could you please clarify this for me.
>
> Thanks
>
> Marie
>
>
>
>
> On 23 May 2006, at 11:12, Robert Oostenveld wrote:
>
>> Hi Marie,
>>
>> On 22 May 2006, at 17:18, Marie Smith wrote:
>>> I have been trying out the various methods as discussed and have
>>> come across a problem.
>>>
>>> When I select cfg.singletrials = 'yes' I get a number of error
>>> messages saying
>>> error('this option contains a bug, and is therefore not supported
>>> at the moment');
>>>
>>> I am using the toolbox fieldtrip-20060516.
>>>
>>> I noticed however, if I select cfg.rawtrials = 'yes' the function
>>> will run.
>>
>> I recall disabling this functionality, since it was rarely used and
>> since I was concerned that it would not be correct. I now had a
>> more detailled look at the code.
>>
>> If you do rawtrial=yes, beamformer uses the single-trial covariance
>> to construct the filter and also applies it to the single trial
>> covariance/csd. That results in a very poorly estimated filter in
>> each trial, hence projecting large amounts of noise and a lot of
>> variance over trials. Therefore we found it not to be very usefull
>> on real data, although conceptually and in the code it is correct.
>>
>> The idea behind singletrial=yes is that beamformer uses the average
>> covariance to construct the filter and applies it to the single
>> trial covariance/csd. The problem in the code however is that
>> beamformer would use the averaged covariance/csd to estimate the
>> power and not the single trial covariance/csd. The estimated single-
>> trial timecourse would be correct, but the power would not be
>> correct. Therefore I disabled that option in the code.
>>
>> The solution is something that you can do yourself in two
>> subsequent runs of sourceanalysis: you can do sourceanalysis on the
>> average (i.e. do not specify any of singletrial/rawtrial options)
>> and specify keepfilter=yes. That will give you the filter, computed
>> on the average covariance. Subsequently do cfg.grid=source2grid
>> (source), and use the resulting grid (including the filters) in the
>> second run of sourceanalysis, in which you specify
>> cfg.rawtrial=yes. In the second run, the previous (based on average
>> covariance) filters will be applied to the unaveraged data,
>> resulting in the desired single-trial power and dipole moment.
>>
>> best regards,
>> Robert
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