I would like to get a mesh outline for my volumetric data, preferably in .ply format. I have found that AFNI’s ConvexHull executable does pretty much what I need, except, of course, that the shape is convex. I am working with mouse brains, which have quite a bit of concavity (though a lot less than the human brain).
Any idea how I can get a nice mesh model from my NIfTI templates?
I may be misunderstanding, but is IsoSurface the function you want? That would make a surface mesh around your volumetric data? It will also output a *.ply file by default, or you can specify “IsoSurface -o_ply PREFIX …” You can apply smoothing as well, with “-Tsmooth …”
SUMA programs will detect which kind of output you want from the file extension, so mysurface.ply will work the same as -o_ply mysurface. This works with IsoSurface for creating surfaces or with ConvertSurface to convert a surface from one format to another. Surfaces can be smoothed (SurfSmooth) or remeshed to a lower resolution too (SurfMesh).