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

[Ying Li]

Dear all,

Thanks so much for all of your enthusiastic replies. I'll give a try to
your suggestions.

Best wishes,

Ying


On Thu, May 22, 2014 at 4:47 AM, Eelke Spaak <eelke.spaak at donders.ru.nl>wrote:

> 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
> >
> >
> > Radboud University Nijmegen
> >
> >
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> >
> >
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> >
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> >
> >
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> >
> >
> > E-Mail: jm.horschig at donders.ru.nl
> >
> >
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> >
> >
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> >
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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
> >
> >
> > J.Schoffelen at donders.ru.nl
> >
> > Telephone: +31-24-3614793
> >
> >
> > http://www.hettaligebrein.nl
> >
> >
> >
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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
> >
> > J.Schoffelen at donders.ru.nl
> > Telephone: +31-24-3614793
> >
> > http://www.hettaligebrein.nl
> >
> >
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