Hi Jonah
no, I don't think that would be very accurate. In our cortical surface
stream we do partial volume modeling in the surface deformation so that
the surface settles at the right point between gray/white and gray/csf.
We never wrote anything comparable for the aseg structs like hippocamp
Hi Bruce,
I'm interested in generating meshes for the whole brain,and individual
regions of the prefrontal cortex and the hippocampus.
It seems that freesurfer doesn't generate meshes with physical volumes
corrected for partial volume effects, but instead performs an a posteriori
calculation that
Hi Jonah
I'm not positive I understand, but I doubt partial volume effects are
isotropic given the geometric complexity of a lot of brain structures.
Maybe the easiest thing for you to do is to use something like SAMSEG in
the upcoming V7 and try deforming the surface to pass through the p=0.5
Hi Bruce,
The issue is that I want the surface mesh itself to reflect the correct
(partial volume corrected) volume as I will be simulating the passage of
high energy particles through it. Do you think it would suffice to take the
(smoothed) mesh and simply scale its volume in an application like
HI Jonah
it depends how you compute volume. mris_volume for example will compute the
volume of the interior without any partial volume correction.
And yes, I would expect you want to smooth the surface a bit. You might try
the Taubin smoothing built into freeview as it won't shrink the surfac
Hi Bruce,
I tried mri_tessellate which worked well in that the surface seems to
follow the aseg projections exactly. Does the volume of this mesh account
for partial volume effects? Also, is there a need to run mri_pretess or
some sort of smoothing procedure?
For reference, what I am trying to do
no, they are definitely not negligible. It depends on structure geometry,
but I bet for something like the hippocampus a large fraction of voxels in
it are partial volumed.
You can use mri_mc or mri_tessellate to generate a mesh. It will be closed
but may not have a simple topology
On Thu, 2
Hi all,
Thanks for the response. I'm familiar with partial volume effects within
the context of PET imaging, but wouldn't you expect these effects to be
negligible in MRI for structures on the order of mm?
With respect to the mesh type, I'd like to get closed meshes for each
segmentation/parcella
Hi Jonah
when we compute volumes we typically use a partial-volume model, which we
have found improves accuracy and repeatability. That may be the source of
your discrepancy
cheers
Bruce
On Wed, 22 Apr 2020, Peter, Jonah wrote:
Hello,
I'm trying to generate surface meshes for different brai
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Could you clarify what kind of meshes you are working with? Are the meshes you
are working with plane-like (parts of the pial surface), or are they closed
(e.g., generating from running marching cubes on a set of cortex voxels)?
Also what is your int
Hello,
I'm trying to generate surface meshes for different brain regions that can
be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ,
etc.). I ran recon-all on my T1 images, and the parcellation/segmentation
looks fine. However, I noticed that when I imported this data into
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