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!
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?
Thank you!
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
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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!
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!
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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Anderson M. Winkler -
Bruce Fischl -
Tanya