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 thesource of
your discrepancy cheers Bruce On Wed, 22 Apr 2020, Peter, Jonah wrote: > Hello, > I'm trying to generate surface meshes for different brainregions 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 this datainto 3DSlicer,
> the volumes of these regions did not match the volumes in theaseg.stats
> file. In some cases, the differences were quite substantial. Itried
> removing all smoothing filters in 3DSlicer but the outcome wasthe same.
> > Do you know what could be going wrong here? Alternatively, isthere an
> easier way to generate surface meshes from the aparc or asegatlases?
> > I'm using the ICBM 2009c Nonlinear Asymmetric > template (http://nist.mni.mcgill.ca/?p=904) as a generic brainvolume
> (though alternative suggestions are welcome). > > Thanks! > Jonah > > -- > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer