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