I put a 1x1 good quality T1 brain through the ANA pipeline (PC version of brainvisa). I get pretty decent 3D mesh's except that there are areas on the white matter mesh where there's a spike sticking out of the brain, and areas where there are "bridges" between gyri that are not supposed to be there. It looks to me like the gray/white segmentation may not have happened perfectly.
what do you think the problem is?
is there a way to fix it? is there a way to edit the segmentation image and re-run the mesh making to fix it?
thanks!!!
Amit
ana do a lot of things...strange "bridges" between
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Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
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Well, it may stem from various sources. Non perfect bias correction (the release to come
should include a much better method, it is really a question of weeks now), some artifact in your data, a poor estimation of the grey/white matter statistics...
There is no simple way to perform correction because the topology of the white matter mesh
has to come from the automatic method. What I would do:
Load the mesh and the voronoi diagram (the mask with split hemispheres) with brainVISA eyes. Click on the problematic area in the 3D viewer of white matter mesh. Observe the corresponding location in the mask thanks to the linked cursor. If there is something bad there, you can edit the mask. Click on the pencil, which will send the mask to the drawing module of Anatomist.
Another approach: open brainVISA treatment in charge of computing the spherical mesh (it is in anatomy/triangulation). Then try to change the pressure parameter to improve the result.
A last approach: click on the eye related to the histogram analysis (file with .han extension). It should open an editor on this simple ASCII file. Try to tune the mean and stabdard deviations of the tissue.
should include a much better method, it is really a question of weeks now), some artifact in your data, a poor estimation of the grey/white matter statistics...
There is no simple way to perform correction because the topology of the white matter mesh
has to come from the automatic method. What I would do:
Load the mesh and the voronoi diagram (the mask with split hemispheres) with brainVISA eyes. Click on the problematic area in the 3D viewer of white matter mesh. Observe the corresponding location in the mask thanks to the linked cursor. If there is something bad there, you can edit the mask. Click on the pencil, which will send the mask to the drawing module of Anatomist.
Another approach: open brainVISA treatment in charge of computing the spherical mesh (it is in anatomy/triangulation). Then try to change the pressure parameter to improve the result.
A last approach: click on the eye related to the histogram analysis (file with .han extension). It should open an editor on this simple ASCII file. Try to tune the mean and stabdard deviations of the tissue.