8000 JavaError in 'nighres.surface.mesh_to_levelset' · Issue #180 · nighres/nighres · GitHub
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JavaError in 'nighres.surface.mesh_to_levelset' #180

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WonderChil opened this issue Apr 5, 2022 · 1 comment
Open

JavaError in 'nighres.surface.mesh_to_levelset' #180

WonderChil opened this issue Apr 5, 2022 · 1 comment

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@WonderChil
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WonderChil commented Apr 5, 2022 •
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Func: nighres.surface.mesh_to_levelset report error as below
Input file is results from FreeSurfer: 'orig.nii.gz' and ('lh.white', 'lh.pial')

Is there any limitation or requirements to use this function? Thanks!

File "....../site-packages/nighres/surface/mesh_to_levelset.py", line 97, in mesh_to_levelset 
        algorithm.execute()
nighresjava.JavaError: <super: <class 'JavaError'>, <JavaError object>>
    Java stacktrace:
**java.lang.ArrayIndexOutOfBoundsException: 1000410**
at de.mpg.cbs.core.surface.SurfaceMeshToLevelsetPseudoNormals.generateEdgeFaceList(SurfaceMeshToLevelsetPseudoNormals.java:589)
at de.mpg.cbs.core.surface.SurfaceMeshToLevelsetPseudoNormals.execute(SurfaceMeshToLevelsetPseudoNormals.java:107)
@piloubazin
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your mesh has to be fully closed, and not contain any pathological triangles (collapsed to a single line or point). We tested it in the past with FreeSurfer meshes, but we may not have covered all possible cases. One possible workaround is to use FreeSurfer's segmentation in voxel space as basis with nighres.surface.probability_to_levelset()
Good luck!

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