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

[Eelke Spaak]

Haha never mind, I was totally confused. "Perpendicular" and
"parallel" both start with a p...

On 22 May 2014 13:42, jan-mathijs schoffelen
<jan.schoffelen at donders.ru.nl> wrote:
> Eelke,
>
> You're absolutely right one should take the orientation that is othogonal!
> In my dictionary this is exactly what the word perpendicular means ;-)...
>
> JM
>
> On May 22, 2014, at 1:25 PM, Eelke Spaak wrote:
>
> 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
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>
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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
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>
> J.Schoffelen at donders.ru.nl
>
> Telephone: +31-24-3614793
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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
>
> http://www.hettaligebrein.nl
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