Hi Bruce, I'm interested in generating meshes for the whole brain,and individual regions of the prefrontal cortex and the hippocampus.
It seems that freesurfer doesn't generate meshes with physical volumes corrected for partial volume effects, but instead performs an a posteriori calculation that is output to the aseg.stats file (is this correct?). What I meant before was: do you think it would be reasonable to take the surface meshes and simply scale down their volumes such that the physical mesh volume then corresponds to the partial volume corrected volume? As an example, suppose the actual physical volume of the hippocampal mesh is 5000 mm3, whereas the aseg.stats lists the volume as 4000 mm3 after correcting for partial volume effects. Would it be correct to just scale the mesh volume to 4000 mm3? Thanks again, Jonah On Fri, Apr 24, 2020 at 10:35 AM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jonah > > I'm not positive I understand, but I doubt partial volume effects are > isotropic given the geometric complexity of a lot of brain structures. > Maybe the easiest thing for you to do is to use something like SAMSEG in > the upcoming V7 and try deforming the surface to pass through the p=0.5 > isosurface. Not sure how hard that would be to implement, maybe others > (Doug? Eugenio? Viviana?) can comment? Are there any specific structures > you are interested in? > > cheers > Bruce > > > On Thu, 23 Apr 2020, Peter, Jonah wrote: > > > 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 <fis...@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 < > 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 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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