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
isosurface. Not sure how hard that would be to implement, maybe others
(Doug? Eugenio? Viviana?) can comment? Are there any specific structures
you are interested in?
cheers
Bruce
On Thu, 23 Apr 2020, Peter, Jonah wrote:
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 blender? My
thinking is that the partial volume effects are probably isotropic so a uniform
scaling would leave the
geometry unchanged.
Best,
Jonah
On Thu, Apr 23, 2020 at 9:53 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
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
<fis...@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
<fis...@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: jonahpe...@g.harvard.edu
> > >
> > >_______________________________________________
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> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > --
> > Jonah PeterGraduate Student in The Biophysics ProgramHarvard
University
> > P: 646-306-0848
> > E: jonahpe...@g.harvard.edu
> >
> >_______________________________________________
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>
>
>
> --
> Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
> P: 646-306-0848
> E: jonahpe...@g.harvard.edu
>
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--
Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
P: 646-306-0848
E: jonahpe...@g.harvard.edu
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