This presentation sums up how to create a
brain model with HyperMesh
The work is based on the results obtain after the work on Slicer3D and IA-FEMesh
Jérémie Voltz
Import your model from IA-FEMesh
Remesh the ventricles
Remesh the elements from brain and tumour with a low
jacobian number (< 0.3)
Integrate the tumour and ventricles in the brain mesh
Create the skull
Create the nodes sets
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Use the exported Abaqus file from IA-FEMesh for the brain
and the tumour
Import just the surface for the ventricles as .stl file
Brain and tumour are 3D meshes and ventricles is considered
as a surface mesh with very high density
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Create a surface based on FE (Geometry > Surfaces)
Clean the surface generated (Geometry > Autocleanup)
◦ Target element size parameter : 5mm
Mesh this surface in another component (2D > Automesh)
Check the length of the new mesh (Tools > Check elems)
◦ No elements should be smaller than 1mm
Remesh manually the small elements by replacing the nodes
(2D > Replace). If too many left to do so, redo the previous
steps
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The model shouldn’t contain any element with a jacobian
smaller than 0.3
Check the elements of your brain (and tumour in a second
time) and save the failed ones
Put them in a new component (Tool > Organize > Elems >
Retrieve)
You can select the adjacent elements too (Elem > By adjacent)
◦ No element should be isolated and the final volume has to be quite thick
for a proper tetras mesh
Extract the faces from this new component (Tool > Faces) and
place them in a new component
This new component contains 2D elements which need to be
cleaned up
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Check the connectivity, duplicates and bad jacobian (<0.3)
elements in this 2D mesh
Delete them (adjacent elements too if necessary), we’ll have
to remesh these parts
You can find the edges with: Tool > Edges
Create surfaces to fill the holes
◦ Based on node list often works
◦ If the spline fails, create a smoothed line first and create the surface based
on the lines
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Remesh the surfaces with triangles
◦ Use the same element size than the parts around
Merge all the nodes to obtain an enclosed volume
◦ Automatic replace by equivalence (Edges > Equivalence)
◦ Manual (2D > Replace, 2D > Split, 2D > Edit Element)
Check that the volume is enclosed with Edges
Mesh this volume with tetras and place them in a new
component (3D > Tetramesh > Tetra Mesh)
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Create a few blocks around the tumour and ventricles which
will be used to select brain elements (Analysis > Blocks)
Put the brain elements inside the blocks in a new component
◦ This component will be the part remeshed with tetras
◦ Make the parts as simple as possible (else the mesh could fail)
Extract the faces of that component
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Extract external faces from the tumour (cf. Creation skull)
Mesh the hole with tetras
◦ Select the two components you want for boundaries
◦ The mesh will stop at the inner component
Check if the nodes of all the useful component are merged
◦ Tool > Edges > Preview Equiv with a low tolerance (0.01)
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Extract faces from all the components visible from the
outside of the brain and COPY them in a new component
Check the connectivity of these faces and delete all failed
elements
◦ These are the faces between each component
Make sure you only have the external faces by looking inside
Check the normals from these faces (Tool > Normals)
◦ Normal should point at inside
◦ Select one element in Orientation and Adjust Normals
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Offset these faces (2D > Elem Offset)
◦ Shell offset: squared corners
◦ Distance: 0.1mm
◦ Offset-
Import the segmented skull which shows the craniotomy
Delete the 2D elements which are visible through the hole
Convert all quads into triangles (2D > Split)
◦ Plate Elements: divide quads
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Nodes sets are used during the simulation
◦ Load-Nodes: surface nodes from brain visible through the hole in the skull
◦ Contact-Nodes: all other surface nodes from the brain
Create the sets (Analysis > Entity Sets) and select the nodes
based on the faces you used for the skull
◦ The nodes have to belong to the brain
Load-Nodes Contact-Nodes
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