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 > > > > > >_______________________________________________ > > 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: jonahpe...@g.harvard.edu > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jonah Peter Graduate Student in The Biophysics Program Harvard University P: 646-306-0848 E: jonahpe...@g.harvard.edu
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