[FieldTrip] Projection from sensors space to segmented brain surface

Thu Jun 21 13:35:42 CEST 2012

Caro Andrea,

You might want to use ft_plot_topo3d for this purpose. This will plot the functional data onto the positions of the channels in 3D, but you need to create the to-be-plotted data as a single vector, and you will need the channel positions in 3D (which you'll get for free when working with MEG data, but which are generally not represented in EEG data). If you concurrently have a cortical reconstruction defined in the same coordinate system as the channels (and in the same metric units (otherwise use ft_convert_units first)), you can do a 'hold on' and use ft_plot_mesh for the visualization of the cortex. I guess that the ft_plot_topo3D has some functionality for transparency.

Ciao,

JM

On Jun 20, 2012, at 8:44 PM, andrea brovelli wrote:

> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> NEW EMAIL: andrea.brovelli at univ-amu.fr
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>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>> 
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>>> 
>> 
>> 
>> ----- Fine messaggio da johanna.zumer at donders.ru.nl -----
>> 
>> 
>> -- 
>> 
>>  NEW EMAIL: andrea.brovelli at univ-amu.fr
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>> 
> 
> 
> ----- Fine messaggio da andrea.brovelli at univ-amu.fr -----
> 
> 
> -- 
> 
>  NEW EMAIL: andrea.brovelli at univ-amu.fr
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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