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Target Outcome

Geometric reconstruction of a tissue of interest ready for meshing:

• as a (parametric or explicit) watertight surface representation, or
• as a solid geometry

Prerequisites

Infrastructure

Previous Protocols

For more details, see Specifications/ImageSegmentation.

Protocols

Input

• Surface representation of tissue of interest in STL format in MRI coordinate system (raw, without filtering and smoothing)

Overview

1. Load the desired STL into Meshlab
2. Perform smoothing procedures on the STL using the component specific procedures described below.
   • Save the STL regularly to avoid losing previous work through program crashes.
3. Perform Paired Mesh distance maping between the RAW and processepd STLs to ensure that there have been no major changes to the mesh.
4. Check and Repair the STL as needed
5. Export the STL. This is now considered to be an explicit surface representation of the tissue of interest processed with volume preserving smoothing.
6. Repeat this process for all components.

Data Input Procedures

IMPORT STL to MeshLab:

1. File -> 'Import Mesh...'

2. Select desired STL file(s) (multiple contiguous by holding 'Shift', multiple non-contiguous by holding 'Ctrl').
3. Click 'Import STL'.

Data Output Procedures

Note: There is no “undo” in MeshLab, and the program crashes often. It is recommended to export the stl after every successful step in the process, to avoid having to repeat steps later!

EXPORT STL from Meshlab

1. Select desired mesh to export from the Layer Dialog panel (see viewing options for directions to display the layer dialog)

2. File -> 'Export Mesh As...'.

3. Name file as desired, with the '.stl' extension.
4. Click 'Save'

Viewing Options

• Select the 'Show Layer Dialog' option.

• During the smoothing process, the layer dialog panel shows the progress, and allows the viewer to select, display, or hide different versions of the mesh. Select the eye toggle next to the mesh name to hide or display it. The body highlighted in yellow is the “current mesh”. Any procedures performed will be applied to the current mesh.

• Select the 'Flat Lines' option to view the mesh lines on the model surface.

General Procedures

Smoothing Procedures (LVTIT)

The protocols for using various smoothing features in MeshLab are described here. Component specific procedures section, below, provides guidelines for which smoothing parameters to use for each tissue type.

Laplacian Smoothing [L]

1. Select desired mesh from the Layer Dialog panel.

2. Filters > 'Smoothing, Fairing and Deformation' > 'Laplacian Smooth'

3. Set smoothing steps to 20 (or other value as per Component-Specific Procedures)
4. Click Apply
5. Save your work!

Surface Reconstruction: VCG [v]

1. Select desired mesh from the Layer Dialog panel.

2. Filters -> 'Remeshing, Simplification and Reconstruction' -> 'Surface Reconstruction: VCG'

3. Set 'Voxel Side', 'world unit' to a meaningful size (i.e. relative to original image resolution; e.g. for cartilage images with a resolution of 0.35 x 0.35 x 0.7 mm, use a world unit of 0.35, 0.5, 0.7 mm).
4. Select 'Post Merge Simplification'.
5. Click 'Apply'.

1. Save your work!

IF STL FRAGMENTS APPEAR AT MODEL EDGES AFTER RECONSTRUCTION:

1. TODO: Describe selecting/deleting floating STL fragments!

NOTES:

• Increasing 'Volume Laplacian iter' decreases resulting reconstructed volume.
• Changing 'Widening' had no visual effect.

Taubin Smoothing [T]

1. Select desired mesh from the Layer Dialog panel.

2. Filters -> 'Smoothing, Fairing and Deformation' -> 'Taubin Smoothing'

3. Select 'Preview' to interactively display current smoothing parameters.
4. Click 'Apply'.

USEFUL FOR:

• Smoothing vertices/nodes at sharply curved model edges.
• Correcting twisted triangles at focal points following 'Iso Parameterization'.

NOTES:

• Suggested settings: Lambda = 0.5, mu = -0.5

• Lambda values > 1.5 cause the mesh to jaggedly explode.

Iso Parameterization [I]

There are 2 stages to Iso Parameterization:

Stage 1: Iso Parameterization

1. Select desired mesh from the Layer Dialog panel.

2. Filters -> 'Remeshing, Simplification and Reconstruction' -> 'Iso Parameterization'

3. Click 'Apply.

IF DOUBLE STEP DOESN'T WORK:

1. Deselect 'Double Step'.
2. Click 'Apply.

WARNINGS:

• This can be buggy, and may cause MeshLab to crash!

• This appears not to be deterministic, i.e. with same input mesh it may or may not work (e.g. same VCG parameters to smooth prior to isoparameterization didn't work in one attempt, but did in another).

Stage 2: Iso Parameterization Remeshing

1. Filters -> 'Remeshing, Simplification and Reconstruction' -> 'Iso Parameterization Remeshing'

2. Try default 'Sampling Rate' = 10.
3. Click 'Apply'.
4. If needed, iterate last two steps, changing the 'Sampling Rate' until desired surface triangle size is obtained.

Paired Mesh Distance Mapping (Hausdorff distance)

1. Import desired STL(s).

COMPUTE DISTANCE MAP:

1. Filters -> Sampling -> Hausdorff Distance.

2. Set the 'Sampled Mesh' to the desired reference surface (i.e. the surface that the colored distance map will be displayed on, mapped at vertices).
3. Set the 'Target Mesh' to the surface used to determine the distance map (from the reference surface vertices).
4. Click 'Apply'.

DISPLAY DISTANCE MAP:

1. Make sure the desired reference map is selected in the Layer hierarchy.

2. Display -> 'Show Vert Quality Histogram'.

3. Filters -> 'Color Creation and Processing' -> 'Color by vertex Quality'.

4. Set 'Min' to 0.
5. Set 'Max' to an appropriate level (suggestion: aim for distance ~zero-count transition in histogram).
6. Select 'Preview' to interactively display currently calculated distance map on the surface.
7. Iterate last three steps until desired color-to-distance correspondence is determined.
8. Click 'Apply'.

Checking and Repairing the STL

After performing the smoothing procedures, it must be checked that the STL is manifold and watertight.

Repair Boundary and Non-Manifold Edges:

1. Select Render > Show Non Manif Edges

2. Select Render> Show Boundary Edges

   • Boxes will pop up showing how many of each of these items exist, and they will be highlighted on the mesh. If these numbers are all zero, skip to check for non manifold edges. If the numbers are non-zero, but you cannot see the highlighted regions on the mesh, select Filters>Selection>Dilate Selection, to help the regions stand out more.

3. For each of the highlighted regions:
   • Use ‘select faces in rectangular region’ tool and select all the faces touching the highlighted region.
     • IMPORTANT! Press alt while using the selection tool so that it will only select the faces on the top layer.
     • Press shift to deselect using the tool
   • Select 'Delete current set of selected faces and vertices' Ignore holes for now.

4. Select Render > Show Non Manif Vertices.

   • A box will pop up showing how many non manifold vertices exist, at this point they should be orphan nodes. If this number is zero, skip to close holes.

5. Select Filters > Cleaning and Repairing > Remove unreferenced vertex

6. Select Filters>Remeshing, Simplification, and Reconstruction > Close Holes. Leave default options and click Apply.

7. Save changes.

Check Directions of Surface Normals:

1. Select Render > Show Face Normals . This will draw a line from the center of all the faces in the direction of the normal. The 3D meshing process will work better if the surface normals all point outward.

2. Select Filter > Normals, Curvatures, and Orientation > Re-Orient all faces coherently

Component-Specific Procedures

Registration Markers

NO Smoothing. Keep the STL in the RAW format

Bones

'General Procedure: Smoothing' (LVTIT) parameters for femur (FMB), tibia (TBB):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.7
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = 10
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

'General Procedure: Smoothing' (LVTIT) parameters for patella (PTB):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.5
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = 7
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

'General Procedure: Smoothing' (LVTIT) parameters for fibula (FBB):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.5
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = 5
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

Cartilage

'General Procedure: Smoothing' (LVTIT) parameters for femoral cartilage (FMC):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = [10,15,20] (low density, mid density, high density)
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

'General Procedure: Smoothing' (LVTIT) parameters for tibial cartilage (TBC-M, TBC-L):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = [7,10,13] (low density, mid density, high density)
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

'General Procedure: Smoothing' (LVTIT) parameters for patellar cartilage (PTC):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = [(6),8,10,(12)] (low density, mid density, high density)
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

Menisci

Modified 'General Procedure: Smoothing' (LIT) parameters for mensici (MNS-M, MSN-L):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [I]soParameterization: Sampling Rate = [6,8,10] (low density, mid density, high density)
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

NOTE: Modified General Procedure preserves volume better for thin, highly curved geometry, but doesn't smooth segmentation aliasing.

Connective Tissue - Ligaments & Tendons

'General Procedure: Smoothing' (LVTIT) parameters for ACL, PCL:

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = [3,4,5] (low density, mid density, high density)
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

'General Procedure: Smoothing' (LVTIT) parameters for patellar ligament (PTL):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = [6,8,10] (low density, mid density, high density)
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

'General Procedure: Smoothing' (LVTIT) parameters for quadriceps tendon (QAT):

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)
4. [I]soParameterization: Sampling Rate = [4,6,8] (low density, mid density, high density)
5. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

Modified 'General Procedure: Smoothing' (LVIT) parameters for MCL:

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [V]CG Surface Reconstruction: Voxel Side (world unit) = 0.35
3. [I]soParameterization: Sampling Rate = [6,7,8] (low density, mid density, high density)
4. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

Modified 'General Procedure: Smoothing' (LIT) parameters for LCL:

1. [L]aplacian Smoothing: Smoothing steps = 20
2. [I]soParameterization: Sampling Rate = [3,4,5] (low density, mid density, high density)
3. [T]aubin Smoothing: Lambda = 0.5, mu = -0.53 (defaults)

Sample Results

Following are images of the three-dimensional knee geometry (at ~90 degree increments) generated by using the coarsest triangulated surfaces.

Output

• Explicit surface representation of tissue of interest; in STL format in MRI coordinate system (processed with volume preserving smoothing)

• Parametric surface representation of tissue of interest in IGES & STP format in MRI coordinate system (processed with volume preserving smoothing)

• Parametric solid model of tissue of interest in IGES & STP format in MRI coordinate system (processed with volume preserving smoothing)