[FieldTrip] SAM beamforming on Neuromag data

Tue May 31 12:42:53 CEST 2011

Dear Elena and group
it basically depends on how much co-variability there is. if you use a large
frequency range and a large strech of time you need to correct little if
any. if you use averaged data and say from 50 to 120ms from target onset you
need more regularization. I used 5% even for relatively short time interval
(but large freq. range) and found it reasonable.
yuval
On 31 May 2011 13:06, Elena Orekhova <Elena.Orekhova at neuro.gu.se> wrote:

>  Hi Michael,
>
>
> > If you run into rank-deficiency issue with the covariance matrix a tiny
> amount of regularization should fix this.
>
> What lambda you would recommend?
>
> Elena
>
>
>  ------------------------------
> *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]
> on behalf of Michael Wibral [michael.wibral at web.de]
> *Sent:* Monday, May 30, 2011 5:58 PM
>
> *To:* Email discussion list for the FieldTrip project
> *Subject:* Re: [FieldTrip] SAM beamforming on Neuromag data
>
>
> Hi Elena,
>
> as far as I can see from the neuromeg discussion list and the maxfilter
> papers the properties of the components removed by the maxfilter do not
> require a leadfield update.
> If you run into rank-deficiency issue with the covariance matrix a tiny
> amount of regularization should fix this.
> (Note: If someone who reads this is of a different opinion, please let me
> know!)
>
>
> Michael
>
>  ------------------------------
> *Von:* "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> *Gesendet:* May 30, 2011 4:30:34 PM
> *An:* "Email discussion list for the FieldTrip project" <
> fieldtrip at donders.ru.nl>
> *Betreff:* Re: [FieldTrip] SAM beamforming on Neuromag data
>
>  Thank you for this.
>
> I have more concerns.  I applied MaxFilter to the data. Since MaxFilter
> reduces the rank of the covariance matrix by removing noisy components, it
> may influence the beamformer results.
> Is it safe to do beamforming with MaxFiltered data?
>
> Elena
>
>  ------------------------------
> *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]
> on behalf of Michael Wibral [michael.wibral at web.de]
> *Sent:* Monday, May 30, 2011 2:08 PM
> *To:* Email discussion list for the FieldTrip project
> *Subject:* Re: [FieldTrip] SAM beamformeing on Neuromag data
>
>
> Hi Elena,
>
> as far as I know, the leadfield computation should be aware of the
> different UNITS (not only scales) of gradiometers and magnetometers. There
> was a problem with the sign of the leadfields but that should have been
> fixed.
>
> There is one more fundamental problem however, that you should be aware of
> (doesn't invalidate your source analysis but bears potential for
> fine-tuning), which is the projection of noise:
> In beamforming the unit gain constraint guarantees that you get your source
> signal back with unit gain. Added on top however is neurophysiological
> crosstalk (minimized) and sensor noise of the sensors with the largest
> weights in your Beamformer (not reducible). So different sensor types
> willhave different (inverse) leadfield strengths, theerfore also fiofefrent
> source noise levels. the relative benefits of each sensor type changes from
> location to location, so a location (and data) dependend weighting would in
> principle be best.
> I am not sure if and how this is implemented if FT (Bayesian weighting
> would be optimal here..)
>
> What you could do as a first step is to beam separately and compare the
> results.
>
> Michael
>
>
>  ------------------------------
> *Von:* "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> *Gesendet:* May 30, 2011 1:08:29 PM
> *An:* "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
> *Betreff:* [FieldTrip] SAM beamformeing on Neuromag data
>
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>
> Dear All,
>
> I try to run beamformer analysis on the auditory MEG data (Neuromag) and
> have basic questions.
>
>
>
> 1.Magnetometers and gradiometers Neuromag sensors have different scales.
> Does the Fieldtrip take care of this difference or should I normalize the
> data?   It yes, how to  normalize?
>
>
>
> 2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs  (virtual channels).  The only tutorial example I have found was for the lcmv-beamformer
> (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure
> which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.
>
>
>
> I would be most grateful for any example script of this type analysis!
>
>
>
> Regards,
>
> Elena
>
>
>
>
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>

-- 
sent from my 4-year-old PC. poor fellow, only ipod classic, no mail there.

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html

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