Hi Tanya,
I think the attached script should do the trick. It calls various FS functions behind the scenes, including mri_tessellate that Bruce was explaining. The outputs will be in a subdirectory called 'ascii' inside each subject directory.
All the best,
Anderson


On 1 June 2014 18:22, Tanya <tanyagl@stanford.edu> wrote:

Thanks Bruce!
Can you please explain how I can view the structure resulting from calling mri_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 vertices 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 work?

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 meshes
> 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!


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