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 > > > >_______________________________________________ > 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-- Jonah PeterGraduate Student in The Biophysics ProgramHarvard University P: 646-306-0848 E: jonahpeter@g.harvard.edu