Hi Jonah
no, I don't think that would be very accurate. In our cortical surface
stream we do partial volume modeling in the surface deformation so that
the surface settles at the right point between gray/white and gray/csf.
We never wrote anything comparable for the aseg structs like hippocampus,
but a quick-and-dirty solution would be to settle at the 0.5 posterior
probablity level of something like samseg
cheers
Bruce
On Fri, 24 Apr
2020, Peter, Jonah wrote:
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
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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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