Hi Tanya
I guess read_surf only supports triangular meshes (which are output by mris_fix_topology). You might try using mri_mc instead (marching cubes), or use freeview -f to visualize it
cheers Bruce On Sun, 1 Jun 2014, Tanya wrote:
Thanks Bruce!
Can you please explain how I can view the structure resulting from calling m ri_tesselate on the left hippocampus in Matlab?
I tried loading it with read_surf.m but the "magic number" doesn't fit - it' s 16777213 instead.
I messed with read_surf.m a bit and forced loading as a QUAD_FILE, but the v ertices matrix looks like this:
-160.2400 0 -158.7600 0 -159.2400 0 -160.0800 0 -158.7600 0 -159.2400 0 -159.9600 0 -158.7600 0 -159.2400 0
....
I can read this into a correct Nx3 coordinate matrix, but I'm not sure what to do with the faces.
Can you maybe help with this? Is there an updated read_surf.m that should wo rk?
Thanks again!
Tanya
sure, you could use mri_tesselate or mri_mc for this. We don't typically generate them as the structures don't really have a surface-based organization so (for example) interior points aren't represented on the mesh
On Fri, 30 May 2014, Tanya wrote:
Hi Freesurfers,I'm wondering whether the meshes (list of vertices+faces) corresponding to structures such as the hippocampus and amigdala are available as part of the Freesurfer output? In the /surf folder there are only the meshes of whole brain structures (cortex, pial, WM...). Is there any utility function to generate the meshe
s
for the smaller structures?
On Fri, May 30, 2014 at 1:18 PM, Tanya tanyagl@stanford.edu wrote: Hi Freesurfers, I'm wondering whether the meshes (list of vertices+faces) corresponding to structures such as the hippocampus and amigdala are available as part of the Freesurfer output? In the /surf folder there are only the meshes of whole brain structures (cortex, pial, WM...). Is there any utility function to generate the meshes for the smaller structures?
Thank you!