Mesh Inspection: Checking Mesh Outputs Before Simulation

Overview

After generating the brain mesh, it is useful to inspect it in LS-PrePost before using it for simulation.

In this step, we will:

1. prepare a visualisation keyword file;
2. open the mesh in LS-PrePost;
3. compare the raw, smoothed, and revised meshes;
4. inspect the part and set definitions.

The main mesh files are:

• mesh.k: Raw voxel-based mesh
• mesh_smoothed.k: Mesh after smoothing
• mesh_smoothed_revised.k: Final mesh after brain–skull contact correction

Additional files used for visualisation:

• part_list_full.k: Reusable part definitions
• set_list.k: Subject-specific set definitions

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1. Preparing the visualisation files

Create a dedicated visualisation folder for the subject:

SUBJECT="sub0045"
mkdir -p data/subjects/${SUBJECT}/visualise

Copy the mesh files and subject-specific set list into this folder:

cp data/subjects/${SUBJECT}/output/mesh.k \
   data/subjects/${SUBJECT}/output/mesh_smoothed.k \
   data/subjects/${SUBJECT}/output/mesh_smoothed_revised.k \
   data/subjects/${SUBJECT}/output/set_list.k \
   data/subjects/${SUBJECT}/visualise/

The set_list.k file is subject-specific because the node and element sets depend on the generated geometry.

The reusable part list is provided in:

src/dependencies/rs/part_list_full.k

Create a wrapper keyword file in the visualisation folder:

touch data/subjects/${SUBJECT}/visualise/visualise_mesh.k

Add the following content to visualise_mesh.k:

*KEYWORD
*INCLUDE
mesh_smoothed_revised.k
*INCLUDE
set_list.k
*INCLUDE
../../../../src/dependencies/rs/part_list_full.k
*END

This wrapper file allows LS-PrePost to load the final mesh together with the part and set definitions.

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2. Opening the mesh in LS-PrePost

Open LS-PrePost and load the wrapper file:

File → Open → Keyword

Select:

visualise_mesh.k

After loading, the mesh should appear in the main graphics window.

Useful controls:

Action	Control
Rotate	Left mouse drag
Pan	Middle mouse drag
Zoom	Scroll wheel
Fit model to screen	Ctrl + F

The main LS-PrePost areas used here are:

• the graphics window, where the mesh is displayed;
• the part display panel, where individual parts can be shown or hidden;
• the message/command window, where loading warnings may appear.

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3. Comparing mesh stages

It is helpful to compare the raw, smoothed, and revised meshes to understand what each processing step has changed.

You can either edit visualise_mesh.k to include a different mesh file, or create separate wrapper files for each stage.

For example:

*KEYWORD
*INCLUDE
mesh.k
*INCLUDE
set_list.k
*INCLUDE
../../../../src/dependencies/rs/part_list_full.k
*END

for the raw mesh.

Raw mesh: mesh.k

The raw mesh is generated directly from the voxel-based pipeline.

Check for:

• overall brain-like geometry;
• both hemispheres present;
• no obvious missing regions;
• expected blocky or stair-step surface.

Smoothed mesh: mesh_smoothed.k

The smoothed mesh should have a cleaner surface.

Check for:

• reduced jagged edges;
• smoother outer surface;
• no excessive shrinkage;
• no obvious surface folding or distortion.

Revised mesh: mesh_smoothed_revised.k

The revised mesh is the final mesh after brain–skull contact correction.

Check for:

• smooth final geometry;
• no obvious brain–skull intersections;
• no visible penetrations or overlapping regions;
• no unexpected holes or gaps.

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4. Inspecting parts and sets

The wrapper file also loads:

part_list_full.k
set_list.k

These make the mesh easier to inspect in LS-PrePost.

Part list

The part list defines the model parts and allows LS-PrePost to display them by part ID or colour.

Use the part display panel to show, hide, or isolate different parts.

Set list

The set_list.k file contains collections of nodes or elements grouped into sets. These are generated during mesh creation and are specific to each subject.

In LS-PrePost, you will typically see two main types:

• A node set is a group of mesh nodes (points in space). In the interface, these appear under: Set → Part
• They are closely related to the part_list_full.k definitions.

What they are used for: - isolating anatomical regions; - assigning material properties; - controlling visibility in LS-PrePost.

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Summary

The final revised mesh should have:

• a plausible brain shape;
• both hemispheres and inferior regions present;
• smooth surface geometry;
• no obvious holes or missing regions;
• no visible brain–skull intersections;
• correctly loaded part and set definitions.

Once these checks look reasonable, the mesh is ready for the simulation setup steps.