[FieldTrip] Different way of calculating the covariance for LCM
Jean-Michel Badier
jean-michel.badier at univmed.fr
Wed Mar 23 09:42:53 CET 2011
Thanks Yuval,
Le 22/03/11 10:55, Yuval Harpaz a écrit :
> So just run the commands on an unaveraged dataset.
>
Yes but that would be correct if there was only one trial in the data
set (see the message from Luisa).
> Another option to consider is the one used by Dr. Robinson when
> performing SAMerf (we have his tool here
> <http://yuval-harpaz.github.com/SAM_BIU/>, works for our 4D machine).
Thanks for it I will test it.
> The idea is to calculate the covariance on all trials, calculate
> weights by this covariance (keep filter in LCMV) and then apply these
> weights on the averaged data. I found it useful because the covariance
> is better for longer datasets, and the averaging in the end increases
> the signal to noise ratio. I do not know exactly how to do it in
> fieldtrip.
>
> On 22 March 2011 10:43, Jean-Michel Badier
> <jean-michel.badier at univmed.fr <mailto:jean-michel.badier at univmed.fr>>
> wrote:
>
> Dear Yuval,
>
> I have to admit that I did not look at the matlab routines.
> In item 2 I suppose that the covariance is calculated for each
> trial then averaged. In item 3 I would like to calculate the
> covariance from all the signal (the trials being concatenated).
>
> Jean-Michel
>
> Le 22/03/11 05:47, Yuval Harpaz a écrit :
>> Dear Jean Michel
>> As far as I know you can do it on an averaged data structure
>> (item 1) or do the same with the data structure before averaging
>> (3). I did not understand what you meant by 2.
>>
>> Yuval
>>
>> On 21 March 2011 22:58, Jean-Michel Badier
>> <jean-michel.badier at univmed.fr
>> <mailto:jean-michel.badier at univmed.fr>> wrote:
>>
>> Dear fieldtrip users,
>>
>> There are different ways of estimating the covariance for
>> LCMV calculation.
>> If I am correct:
>>
>> 1. As suggested in one of the tutorial one can apply the
>> calculation of the covariance directly on the average data
>> (for the different periods of interest that are at least a
>> base line and the period of interest).
>>
>> 2. Estimate the covariance from the average of the covariance
>> rather than the covariance of the average using
>> cfg.keeptrials = "yes"
>>
>> 3. Estimate the covariance from the whole trials concatenated
>> together.
>> Is there an easy way to do that in fieldtrip (beside create a
>> new data set of one trial constituted of all the trials)?
>>
>> Thanks
>>
>> Jean-Michel
>>
>> --
>>
>> Jean-Michel Badier PhD
>>
>>
>> Laboratoire de MagnétoEncéphaloGraphie
>>
>> INSERM U751. Aix Marseille Université
>>
>> 33 (0)4 91 38 55 62
>>
>> _jean-michel.badier at univmed.fr_
>> <mailto:jean-michel.badier at univmed.fr>
>>
>>
>> Service de Neurophysiologie Clinique. CHU Timone
>>
>> 264 Rue Saint-Pierre, 13005 Marseille-France
>>
>>
>>
>>
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>>
>>
>>
>>
>> --
>> Y.Harpaz
>>
>> a link to the BIU MEG lab:
>> http://faculty.biu.ac.il/~goldsa/index.html
>> <http://faculty.biu.ac.il/%7Egoldsa/index.html>
>>
>> " Why, Dan," ask the people in Artificial Intelligence, "do you
>> waste your time conferring with those neuroscientists? They wave
>> their hands about information processing and worry about where
>> it happens, and which neurotransmitters are involved, and all
>> those boring facts, but they haven't a clue about the
>> computational requirements of higher cognitive functions."
>> "Why," ask the neuroscientists, "do you waste your time on the
>> fantasies of Artificial Intelligence? They just invent
>> whatever machinery they want, and say unpardonably ignorant
>> things about the brain." The cognitive psychologists, meanwhile,
>> are accused of concocting models with neither biological
>> plausibility nor proven computational powers; the anthropologists
>> wouldn't know a model if they saw one, and the philosophers, as
>> we all know, just take in each other's laundry, warning about
>> confusions they themselves have created, in an arena bereft of
>> both data and empirically testable theories. With so many idiots
>> working on the problem, no wonder consciousness is still a
>> mystery./Philosopher Daniel Dennet, consciousness explained, pp. 225/
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> --
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html
> <http://faculty.biu.ac.il/%7Egoldsa/index.html>
>
> " Why, Dan," ask the people in Artificial Intelligence, "do you waste
> your time conferring with those neuroscientists? They wave their hands
> about information processing and worry about where it happens, and
> which neurotransmitters are involved, and all those boring facts, but
> they haven't a clue about the computational requirements of higher
> cognitive functions." "Why," ask the neuroscientists, "do you waste
> your time on the fantasies of Artificial Intelligence? They just
> invent whatever machinery they want, and say unpardonably ignorant
> things about the brain." The cognitive psychologists, meanwhile, are
> accused of concocting models with neither biological plausibility nor
> proven computational powers; the anthropologists wouldn't know a model
> if they saw one, and the philosophers, as we all know, just take in
> each other's laundry, warning about confusions they themselves have
> created, in an arena bereft of both data and empirically testable
> theories. With so many idiots working on the problem, no wonder
> consciousness is still a mystery./Philosopher Daniel Dennet,
> consciousness explained, pp. 225/
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
--
Jean-Michel Badier
Laboratoire de MagnétoEncéphaloGraphie
INSERM U751. Aix Marseille Université
33 (0)4 91 38 55 62
_jean-michel.badier at univmed.fr_ <mailto:jean-michel.badier at univmed.fr>
Service de Neurophysiologie Clinique. CHU Timone
264 Rue Saint-Pierre, 13005 Marseille-France
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