[FieldTrip] Projection from sensors space to segmented brain surface
andrea brovelli
andrea.brovelli at univ-amu.fr
Thu Jun 21 13:46:12 CEST 2012
Thank you all for your help.
Andrea
----- Message de jan.schoffelen at donders.ru.nl ---------
Date : Thu, 21 Jun 2012 13:35:42 +0200
De : jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
Répondre à : FieldTrip discussion list <fieldtrip at science.ru.nl>
Objet : Re: [FieldTrip] Projection from sensors space to segmented
brain surface
À : FieldTrip discussion list <fieldtrip at science.ru.nl>
> 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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>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
>>>
>>>
>>> ----- Fine messaggio da johanna.zumer at donders.ru.nl -----
>>>
>>>
>>> --
>>>
>>> NEW EMAIL: andrea.brovelli at univ-amu.fr
>>> _______________________________________________
>>> fieldtrip mailing list
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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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