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
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
Hi Bruce,
That was very quick! Yes, I do believe this is what I am looking for. Thank you so much!
Best Daniel
On Fri, Nov 13, 2015 at 4:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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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Daniel Lindh