Hi Daniel

do you mean the white and pial surfaces? You can certainly compute the
surface normals for them, or use mris_convert to do it:

mris_convert -n lh.white lh.white.normals.asc


will compute and write out the surface normals (using an outwards-pointing
convention) for the white surface to an ascii file

cheers
Bruce

On Fri, 13 Nov 2015,
Daniel Lindh wrote:

> Hi,
> I am looking for a way of figuring out the orientation vector of the neurons
> within a voxel. That is, in which direction is the dipole of the neurons
> pointing at. This could be possible to calculate if there is a way of
> determining the position of the inner and outer layer for each voxel, which
> I am assuming is something Freesurfer does when it calculates gray matter
> thickness. If you could direct me to some relevant literature or an online
> tutorial I would be extremely grateful.
>
> best regards
> Daniel
>
>

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