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 fischl@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 fischl@nmr.mgh.harvard.edu
wrote:
no, they are definitely not negligible. It depends on structuregeometry,
but I bet for something like the hippocampus a large fraction ofvoxels in
it are partial volumed. You can use mri_mc or mri_tessellate to generate a mesh. It willbe 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 volumeeffects within the context of
PET imaging, but > wouldn't you expect these effects to be negligible in MRI forstructures on the order of
mm? > > With respect to the mesh type, I'd like to get closed meshes foreach
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-volumemodel, which we
> have found improves accuracy and repeatability. That maybe the source of
> your discrepancy > > cheers > Bruce > On Wed, 22 Apr 2020, Peter, Jonah wrote: > > > Hello, > > I'm trying to generate surface meshes for differentbrain 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 theparcellation/segmentation
> > looks fine. However, I noticed that when I imported thisdata into 3DSlicer,
> > the volumes of these regions did not match the volumesin the aseg.stats
> > file. In some cases, the differences were quitesubstantial. I tried
> > removing all smoothing filters in 3DSlicer but theoutcome 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 oraseg atlases?
> > > > I'm using the ICBM 2009c Nonlinear Asymmetric > > template (http://nist.mni.mcgill.ca/?p=904) as ageneric brain volume
> > (though alternative suggestions are welcome). > > > > Thanks! > > Jonah > > > > -- > > Jonah PeterGraduate Student in The BiophysicsProgramHarvard University
> > P: 646-306-0848 > > E: jonahpeter@g.harvard.edu > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > -- > Jonah PeterGraduate Student in The Biophysics ProgramHarvardUniversity
> P: 646-306-0848 > E: jonahpeter@g.harvard.edu > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Jonah PeterGraduate Student in The Biophysics ProgramHarvard University P: 646-306-0848 E: jonahpeter@g.harvard.edu
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