TableOfContents()

Target Outcome

Geometric reconstruction of a tissue of interest ready for meshing:

Prerequisites

Include(Infrastructure/AuxiliarySoftware, "Infrastructure", 2, from="= Geometry & Mesh Generation & Manipulation =", to="= Scripting & Numerical Analysis =")

Previous Protocols

For more details, see ["Specifications/ImageSegmentation"].

Protocols

Input

Procedures

-- ["aerdemir"] DateTime(2013-12-30T15:14:36Z) This section may list general purpose procedures and alternatives to utilize the same input to reach the same output. Procedures optimized for specific tissues should also be provided in here.

When starting with volume representation

When starting with surface representation

When parametric geometry is needed

Slicer Procedures

Generate Triangulated Surface (STL) with Laplacian Smoothing

MeshLab Procedures

Input/Output

IMPORT STL:

  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'.

EXPORT STL:

  1. Select desired mesh to export from the Layer hierarchy (display by selecting 'stack of planes' icon above 3D viewport).

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

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

Remeshing, Simplification and Reconstruction

Surface Reconstruction: VCG
  1. Select desired mesh from the Layer hierarchy 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'.

IF STL FRAGMENTS APPEAR AT MODEL EDGES AFTER RECONSTRUCTION:

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

NOTES:

Iso Parameterization
  1. Select desired mesh from the Layer pane.

  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:

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.

Smoothing

Taubin Smoothing

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

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

USEFUL FOR:

NOTES:

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'.

Blender Procedures

Input/Output

IMPORT STL:

  1. File -> Import -> 'Stl (.stl)'.

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

EXPORT STL:

  1. Select the desired mesh to export from the hierarchical Outliner editor pane (default: upper right).

  2. File -> Export -> 'Stl (.stl)'

  3. Specify a desired folder and filename (extension: .stl).
  4. Click 'Export STL'.

Useful Shortcuts

3D Viewport Interaction

Triangulated surface mesh (STL) splitting

In order to determine tissue thickness for thin structures (e.g. cartilage, ligament, tendon) using MeshLab, the manifold (water-tight) triangulated surface mesh must be split into to non-manifold, complementary shells. The procedure to do this is as follows:

  1. Import desired STL(s).
  2. Ensure you are in 'Object Mode' (shown in drop-down menu underneath the 3D Viewport).
  3. Selected the desired STL with one of the following options:
    1. In the 'Outliner' panel (default: upper right), showing the scene graph and datablocks hierarchy, left-click the desired STL.
    2. In the 3D View, right-click on the desired STL interactively.
  4. Hit 'Tab' to change to 'Edit Mode'.
  5. Make sure 'Face Select' mode is selected:
    • in the 3D Viewport menu (underneath), left-click the icon showing a cube with one orange face (in a group of three icons, in the ).
  6. Press 'a' to deselect all faces (automatically selected by default when entering 'Edit Mode').
  7. SELECT DESIRED SET OF CONTIGUOUS TRIANGLES:
    • Right-click a single triangular face on the desired side of the thin model component.

    • In 3D Viewport menu -> Select -> 'Linked Flat Faces':

    • Adjust Sharpness (angle: degrees) until the desired set of contiguous triangular faces are obtained (determine the max. angle that includes the largest region of one side of the thin structure, without spilling over onto the opposite face of the structure).
    • MODIFY SELECTION, IF NEEDED:
      1. Add/select 'holes' (unselected triangles) in contiguously selected region: use 'Circle Select' or 'Lasso Select'
      2. Tidy boundary of select contiguous triangles: use 'Circle Select'
  8. PARTITION STL MESH:
    • Press 'p' ('Separate').

    • From Pop-up menu -> 'Selection P'

Component-Specific Procedures

General Procedure (a.k.a. LVTIT)

  1. Slicer:

    1. Load desired segmented label map/image volume.
    2. Generate triangulated surface (STL) from desired component using 'Laplacian Smoothing' [L] (Smooth = 20, Decimate = 0, 'Post Merge Simplification'), to provide maximum mesh volume prior to following processing steps, which tend to shrink the volume.

  2. Meshlab:

    1. Load STL generated in prior step.
    2. Perform 'Surface Reconstruction: VCG' [V] ('Voxel Side'(world unit) = 0.35-0.7), to smooth out step-i-ness of mesh.
    3. Perform 'Taubin Smoothing' [T] (Lambda = 0.5, mu = -0.5), to make discretized triangules more uniform in areas of high curvature or triangle node density.
    4. Perform 'Iso Parametrization' [I].
    5. Perform 'Iso Parametrization Remeshing' (Sampling rate = 5-15).
    6. Perform 'Taubin Smoothing' [T] (Lambda = 0.5, mu = -0.5), to untwist potentially collapsed triangles at focal points from iso parametrization.

Registration Markers

Bones

'General Procedure' parameters for femur, tibia:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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' parameters for patella:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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' parameters for fibula:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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' parameters for femoral cartilage:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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' parameters for tibial cartilage:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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' parameters for patellar cartilage:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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' parameters for mensici:

  1. [L]aplacian Smoothing: Smooth = 20, Decimate = 0, 'Post Merge Simplification'
  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)

Connective Tissue - Ligaments & Tendons

Results

Following are examples (oks001) of distance maps (using MeshLab: Hausdorf distance) between various pairs of surfaces to assess:

  1. spatial error between corresponding surfaces with varying levels of smoothing/refinement
  2. distance between different model components (e.g. femur vs. femur cartilage, BACK SURFACE)
  3. thickness of model components (e.g. cartilage):

To map tissue thicknesses (e.g. cartilage), opposing surfaces (i.e. BACK SURFACE, FRONT SURFACE) from a manifold (i.e. watertight) STL mesh were split into two complementary, shell STL mesh sets using Blender.

NOTE: all units are displayed in mm.

Smoothing Errors

UNSMOOTHED vs. SMOOTHED:

Distance between Model Components

FEMUR vs. FEMUR CARTILAGE:

FEMUR CARTILAGE vs. FEMUR:

Tissue Thickness

FEMUR CARTILAGE THICKNESS (UNSMOOTHED):

FEMUR CARTILAGE THICKNESS (VCG smoothed, 0.7):

FEMUR CARTILAGE THICKNESS (VCG smoothed, 0.7; ISO, 10):

FEMUR CARTILAGE THICKNESS (LVTIT):

NOTE: spurious distances (0.0 mm, which are known not to be correct) are present only in the FRONT SURFACE (REF) vs BACK SURFACE, despite similar relative normal directions between reference and measured surfaces!!!

Output