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 surface,
but you can also try mris_smooth

cheers
Bruce


On Thu, 23 Apr 2020, Peter, Jonah wrote:

> 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 is import these surface meshes into a Geant4 simulation for proton
> therapy, and want to make sure I'm using as realistic geometry as possible. Ideally I'd be able to
> generate a mesh for the whole brain as well as individual segmentations.
>
> Thanks again for your help,
> Jonah
>
> On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       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, 23 Apr 2020, Peter, Jonah
>       wrote:
>
>       > 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/parcellation.
>       >
>       > Is there a way to do this in freesurfer?
>       >
>       > On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       >       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 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 3DSlicer,
>       >       > the volumes of these regions did not match the volumes in the aseg.stats
>       >       > file. In some cases, the differences were quite substantial. I tried
>       >       > removing all smoothing filters in 3DSlicer but the outcome was the same.
>       >       >
>       >       > Do you know what could be going wrong here? Alternatively, is there an
>       >       > easier way to generate surface meshes from the aparc or aseg atlases?
>       >       >
>       >       > I'm using the ICBM 2009c Nonlinear Asymmetric
>       >       > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume
>       >       > (though alternative suggestions are welcome).
>       >       >
>       >       > Thanks!
>       >       > Jonah
>       >       >
>       >       > --
>       >       > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
>       >       > P: 646-306-0848
>       >       > E: jonahpeter@g.harvard.edu
>       >       >
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>       >
>       >
>       > --
>       > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
>       > P: 646-306-0848
>       > E: jonahpeter@g.harvard.edu
>       >
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> --
> Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
> P: 646-306-0848
> E: jonahpeter@g.harvard.edu
>
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