[FieldTrip] Projection from sensors space to segmented brain surface

[andrea brovelli]

Otherwise, to make things easier: is there a simple way to visualise a  
given topography in 3D (rather than in a 2D layout as done with  
ft_topoplotTFR) together with different segmented surfaces such as the  
skin or the brain meshes ?

Thanks

Andrea


----- Messaggio da andrea.brovelli at univ-amu.fr ---------
     Data: Wed, 20 Jun 2012 18:56:58 +0200
     Da: andrea brovelli <andrea.brovelli at univ-amu.fr>
Rispondi-A: FieldTrip discussion list <fieldtrip at science.ru.nl>
  Oggetto: Re: [FieldTrip] Projection from sensors space to segmented  
brain surface
       A: FieldTrip discussion list <fieldtrip at science.ru.nl>


> Thank you very much for your quick reply, Eelke and Johanna.
>
> Yes, I would like only to visualise the data on a cortical surface  
> and I am aware of the potential misinterpretation of such  
> visualisation.
>
> I would like to use it as an intermediate step between the  
> ft_topoplot on 2D layout and proper source localisation. It would  
> serve as an exploratory tool to decide at which frequency, say, I  
> would do a beamforming and to have a very rough idea of the number  
> and location of cortical sources.
>
> However, it is not very clear to me how I could do this using the  
> example in the beamforming tutorial. Could you be a bit more  
> explicit ? Should I need to do source reconstruction for  
> visualisation ?
>
> Thanks a lot
>
> Andrea
>
>
> ----- Messaggio da johanna.zumer at donders.ru.nl ---------
>     Data: Wed, 20 Jun 2012 18:22:48 +0200
>     Da: Johanna Zumer <johanna.zumer at donders.ru.nl>
> Rispondi-A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>  Oggetto: Re: [FieldTrip] Projection from sensors space to segmented  
> brain surface
>       A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>> Dear Andrea,
>>
>> I would like to further clarify the options for this question.    Perhaps
>> could you suggest which inverse algorithm you had in mind?
>>
>> For example, it is possible to use beamforming limited only to voxels
>> defined as lying on the cortical sheet (i.e. restrict .inside to be only
>> the gray matter).   This is possible, but you might miss out on the spatial
>> peak of the source lying just 5mm away to the inside a bit.   Thus, it
>> would be better to do as Eelke suggested and apply beamforming to the whole
>> inside of the brain, and then project those values to the surface for
>> visualisation (which is easily done with the cfg.method='surface' option in
>> ft_sourceplot).
>>
>> Alternatively, you can use a min-norm type of inverse method (e.g. sLORETA
>> or MNE) which are commonly used to reconstruct onto cortical surface voxels
>> only.  This works because the min-norm algorithms force all activity to lie
>> in the region over which you select to reconstruct.  Thus, a source 5mm
>> inside of the surface will automatically get projected to the surface.
>>
>> I also agree with Eelke you should not just project sensors to surface
>> without doing a specific type of inverse method.
>>
>> Cheers,
>> Johanna
>>
>> 2012/6/20 Eelke Spaak <eelke.spaak at donders.ru.nl>
>>
>>> Dear Andrea,
>>>
>>> If I understand your question correctly, you just want to *visualise*
>>> sensor space activity on a brain surface, without doing source
>>> reconstruction first? I would advise against this. Time-frequency
>>> power values of your planar gradient data reflect the spectral
>>> characteristics of the magnetic gradient at the location of your
>>> sensors. These sensors are not located at the surface of the brain,
>>> but quite some centimeters away from it. Therefore, visualising the
>>> data as if it were actually recorded on the brain surface, without
>>> doing a proper transformation, is potentially misleading. It is true
>>> that people tend to display all sorts of data in a 'topoplot' fashion,
>>> but in that case it is clear to the audience that you are looking at a
>>> representation in sensor-space. Have a look at ft_topoplotTFR for this
>>> approach, if you're not already familiar with it.
>>>
>>> If you want to display your time-frequency activity on a cortical
>>> surface (which is of course a perfectly valid thing to want to do),
>>> you first should map the sensor activity to source space. This mapping
>>> is non-trivial and can be done by e.g. beamforming. See
>>> http://fieldtrip.fcdonders.nl/tutorial/beamformer for a tutorial on
>>> this. That tutorial ends with a surface plot.
>>>
>>> Hope this helps!
>>>
>>> Best,
>>> Eelke
>>>
>>> On 20 June 2012 17:26, andrea brovelli <andrea.brovelli at univ-amu.fr>
>>> wrote:
>>>>
>>>> Dear Fieldtrip users and developpers,
>>>>
>>>> I would like to project and visualise time-frequency power values
>>> computed
>>>> on planar gradient data at the sensors level onto the brain surface
>>>> segmentated from the anatomial MRI of the subject.
>>>>
>>>> Can anyone suggest me how to do it in Fieldtrip ? Can anyone share the
>>>> scripts ?
>>>>
>>>> Does anyone see any inconvenient to this visualisation ?
>>>>
>>>> Thanks a lot for you help.
>>>>
>>>> Andrea
>>>>
>>>>
>>>>
>>>> --
>>>>
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>>
>
>
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>
>
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