Holes in white matter mesh

Questions about BrainVisa usage and installation

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Olivier Coulon
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Joined: Fri Feb 27, 2004 11:48 am
Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France

Holes in white matter mesh

Postby Olivier Coulon » Wed Jul 25, 2018 4:57 pm

this post is just to point out something I noticed while importing unusual data, i.e. chimpanzee data that have been segmented with a different software.

I imported segmentations into BV, ran the missing step, etc... Then I ran the topological corrections, then the grey/white mesh extraction. I got a number of holes in the surface. On the other hand when I replace this last step by the process 'white mesh without decimation' I do not get them. The only difference between the two methods are the parameters of 'AimsMeshBrain'. So this process can generate holes in a spherical surfaces I guess. I thought it would be worthwhile pointing out. Below is an image pointing out the holes (red arrows). In green is the result of 'WM without decimation', in grey is the standard Morphologist mesh, with holes.


Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france

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Re: Holes in white matter mesh

Postby riviere » Wed Aug 15, 2018 9:08 pm

Hi Olivier,
Sorry I didn't see your post, the forum notification seems broken...
Well, what you're saying is a bit frightening... If the decimation process creates holes in meshes, it's not normal at all. The algorithm hasn't been modified in decades so all meshes ever created by brainvisa might be affected.
Do you have an example that you can send me, with an explanation on where I can see the problem ?

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