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
>
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