[FieldTrip] Generate a source model where dipoles are perpendicular to the cortex surface

[Eelke Spaak]

Hi Ying & JM & the rest of the list,

I've never worked with cortex-constrained source reconstructions
before, but one question came to mind: doesn't it make more sense to
constrain the dipole orientations to *orthogonal* to the cortex,
rather than perpendicular? Given that currents along the aligned
dendrites of L5 pyramidal cells are (afaik) likely the most important
origin of the MEG signal, and those dendrites are oriented
approximately orthogonal to the cortical surface, isn't that what you
would expect?

Best,
Eelke

On 22 May 2014 11:47, jan-mathijs schoffelen
<jan.schoffelen at donders.ru.nl> wrote:
> Hi Ying,
>
> Yes, it's possible to constrain the dipole orientation. If you have a
> cortical sheet based source model that contains a triangulation that
> describes the topology, it's in principle possible to compute the
> orientation perpendicular to the sheet (this can e.g. be done  by the
> 'normals' function which I believe should be in ~/fieldtrip/private).
> Subsequently, for each vertex in the cortical sheet you can multiply the
> leadfield matrix with this vector to get a single column leadfield vector
> per vertex that describes the sensor topography of a dipolar source with
> orientation perpendicular to the cortex.
>
> Best,
> Jan-Mathijs
>
> On May 22, 2014, at 11:04 AM, Eelke Spaak wrote:
>
> Hi Ying,
>
> In addition to this, of course first you would need a model of the
> cortical surface for your subjects. See
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate for how to
> obtain such a model (using FreeSurfer) and getting it into FieldTrip.
>
> Best,
> Eelke
>
> On 22 May 2014 10:56, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:
>
> Hi Ying,
>
>
> when computing the leadfields you can set the option cfg.reducerank, which
>
> 'nulls' the dimension(s) which explain(s) the least variance (this is not
>
> quite true, but figuratively speaking). I think this is what comes closest
>
> to what you are looking for. There is no way to explicitly set desired
>
> orientations to zero apart from modifying the leadfield structure yourself.
>
> But that should be easily achievable, right?
>
>
> Best,
>
> Jörn
>
>
>
> On 5/22/2014 10:26 AM, Ying Li wrote:
>
>
> Dear all,
>
>
> I tried to use fieldtrip to generate a source space and calculate lead
>
> field matrix. I found that the dipoles in the source space has x, y, z
>
> orientations. Is it possible to generate a source model where the dipole is
>
> perpendicular to the cortex surface?
>
>
> Actually this can be very helpful, since it will reduce the unknown
>
> variables and make the inverse problem easier to solve. Also, there are some
>
> inverse algorithms which require the dipole to be perpendicular to the
>
> cortex surface.
>
>
> Thanks a lot!!!
>
>
> Best,
>
>
> Ying
>
>
>
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> --
>
> Jörn M. Horschig
>
> PhD Student
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Centre for Cognitive Neuroimaging
>
> Radboud University Nijmegen
>
> Neuronal Oscillations Group
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> FieldTrip Development Team
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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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> http://www.hettaligebrein.nl
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