you can also
Convert a surface file to ascii (vertices are surface normals):
mris_convert -n lh.white lh.white.normals.asc
On 8/20/2022 8:41 AM, Yendiki, Anastasia wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi
<qi.z...@icahn.mssm.edu>
*Sent:* Saturday, August 20, 2022 8:33 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] primary diffusion direction & surface
normal vector
External Email - Use Caution
Hi Anastasia,
Thanks for your prompt reply. So can the normal vector of a surface be
found in the outputs of recon-all?
Best,
Qi
On Sat, Aug 20, 2022 at 8:28 AM Yendiki, Anastasia
<ayend...@mgh.harvard.edu> wrote:
The principal eigenvector of the tensor, which is the primary
direction of diffusion, is V1. The magnitude of that vector is L1,
i.e., AD.
The normal vector of a surface is a vector perpendicular to the
tangent plane to the surface at a certain point. It's a
characteristic of a surface, rather than a characteristic of
diffusion, so you won't find it among the outputs of the diffusion
tensor fit.
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi
<qi.z...@icahn.mssm.edu>
*Sent:* Friday, August 19, 2022 1:55 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] primary diffusion direction & surface
normal vector
External Email - Use Caution
Hi Freesurfer experts,
After DTI tensor fitting, usually we obtain primary, secondary,
and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2,
L3). So what do we use to describe the primary diffusion
direction, FA or AD(=L1)? I read the term "surface normal vector"
from a paper and the formula r=[Vn * e1|. V presents the surface
normal vector, which can be computed using the cross-product
between edges. Where can I find this information?
The paper named: "Surface-based analysis of diffusion orientation
for identifying architectonic domains in the in vivo human cortex"
Thank you so much!
Best,
Qi
--
Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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