3 Matictutorial

Version 13.
0 - Tutorial
3-matic Research 13.0 – Tutorial – L-10788-01
Content
Content .......................................................................................................................... 1
/ Introduction to 3-matic Research .................................................................... 3
/ Chapter 1: Import .............................................................................................. 4
Exercise 1. Import STLs ................................................................................................ 4
Exercise 2. Import a Mimics project file .......................................................................... 5
Exercise 3. Import a CAD file of a heart valve ................................................................ 5
/ Chapter 2: Basic ................................................................................................ 6
Exercise 1: Align the heart valve with the aorta.............................................................. 6
/ Chapter 3: Analyze ............................................................................................ 8
Exercise 1. Wall Thickness Analysis .............................................................................. 8
Exercise 2. Curvature Analysis .....................................................................................10
Exercise 3. Part Comparison Analysis ..........................................................................11
Exercise 4. Measure and analyze using fitted primitives ...............................................13
/ Chapter 4: Design ............................................................................................ 16
Exercise 1. Give the aorta a thickness for additive manufacturing ................................16
Exercise 2. Aneurysm design .......................................................................................17
Exercise 3. Designing an acetabular cup ......................................................................18
Exercise 4: Creating a Custom Cardiovascular Benchtop Model ..................................28
Task 1. Clean and Optimize the Geometry .............................................................................. 29
Task 2. Add a Thickness and Trim the Model .......................................................................... 29
Task 3. Design Base and Supports .......................................................................................... 30
Task 4. Add a flange to the benchtop model ............................................................................ 34
Task 5. Apply Finishing Touches and Export ........................................................................... 36
Exercise 5. Design of a patient specific cranial plate.....................................................37
Task 1. Indicate the outline of the gap ...................................................................................... 38
Task 2. Mirror the healthy geometry and create a guiding line ................................................ 40
Task 3. Creation of the cranial plate ......................................................................................... 44
Task 4. Removing the undercuts .............................................................................................. 47
Task 5. Creating a smooth edge and chamfered edge ............................................................ 48
Task 6. Creating suture holes ................................................................................................... 49
/ Chapter 5: Remesh .......................................................................................... 52
Basic explanation of the finite element method .............................................................52
Element quality .............................................................................................................52
Typical Remesh workflow .............................................................................................53
Tips and tricks ..............................................................................................................54
Exercise 1. Introduction to the workflow ........................................................................55
Task 1. Import and visualize the mesh ..................................................................................... 55
Task 2. Reduce the details of the anatomical part ................................................................... 56
Task 3. Remesh the surface elements ..................................................................................... 56
Task 4. Generate the volume mesh ......................................................................................... 56
Task 5. Material assignment ..................................................................................................... 57
Exercise 2. Inspect mesh quality...................................................................................62
Task 1. Inspect the quality of the surface mesh ....................................................................... 62
Task 2. Remesh the surface elements ..................................................................................... 63
Task 3. Further improve the mesh by Smoothing .................................................................... 64
Task 4. Generate a Tet10 volume mesh .................................................................................. 65
Task 5. Inspect the quality of the volume mesh ....................................................................... 66
Exercise 3. Local mesh refinement ...............................................................................67
Task 1. Surface refinement ...................................................................................................... 67
Task 2. Volume refinement ....................................................................................................... 69
Exercise 4. Gradient Remesh .......................................................................................70
Exercise 5. Creating a Midplane mesh .........................................................................72
Non-manifold Assembly ................................................................................................74
Materialise NV I Technologielaan 15 I 3001 Leuven I Belgium I mimics@materialise.be I materialise.com

Exercise 6. Creating Non-manifold Assembly for anatomical parts ...............................75

Task 1. Generate Non-manifold Assembly in Mimics Research .............................................. 75
Task 2. Reduce details and Remesh the surface elements ..................................................... 76
Task 3. Create volume mesh .................................................................................................... 78
Task 4. Material assignment ..................................................................................................... 78
Exercise 7. Creating Non-manifold Assembly for intersecting parts ..............................81
Exercise 8. Creating a Non-manifold Assembly with a grid ...........................................84
Task 1. Creating the non-manifold assembly ........................................................................... 84
Task 2. Reducing the number of triangles ................................................................................ 84
Exercise 9. Improving the accuracy of the grid-based method ......................................87
Task 1. Creating the non-manifold assembly ........................................................................... 87
Task 2. Improving the accuracy of the screw ........................................................................... 88
Task 3. Dealing with intersecting triangles ............................................................................... 88
Task 4. Improving the mesh ..................................................................................................... 90
Task 5. Creating volume mesh and identifying bad volume elements ..................................... 91
Exercise 10. Exporting and importing the mesh into a solver program ..........................94
Task 1. Generating a mesh with material properties ................................................................ 94
Task 2. Exporting the mesh to ANSYS® Workbench™ ............................................................. 97
Exporting a file to ANSYS® Workbench™ version 14.0 or earlier ............................................ 100
Exporting a file to ABAQUS/CAETM ........................................................................................ 100
Exporting a file to COMSOL Multiphysics® ............................................................................. 101
Exporting a file to MSC Patran®.............................................................................................. 102
/ Chapter 6: Texturing ..................................................................................... 103
Introduction to the Texturing module...........................................................................103
Exercise 1: Applying a Texture to an Imported STL ....................................................103
Task 1. Import the file ............................................................................................................. 103
Task 2. Create a surface for texturing .................................................................................... 103
Task 3. Apply the 2D texture .................................................................................................. 106
Task 4. Convert to a 3D texture .............................................................................................. 108
/ Chapter 7: Export .......................................................................................... 109
Exercise 1: Anatomical Reverse Engineering .............................................................109
Exercise 2: Export 3D PDF .........................................................................................111

/ Introduction to 3-matic Research
3-matic Research is unique software that combines CAD tools with pre-processing (meshing)
capabilities. To do so, it works on triangulated (STL) files and as such it is extremely suitable for
organic/freeform 3D data, like the anatomical data coming from the segmentation of medical images
(from Mimics Research). We call it Anatomical CAD.
Import your anatomical data in 3-matic Research to start doing real Engineering on Anatomy, like
thorough 3D measurements and analyses, design an implant or surgical guide within a research context,
or prepare the mesh for finite element modeling.
Since 3-matic Research can import CAD data, but also do reverse engineering of anatomical data to
CAD data, it is perfectly complementary to your CAD package.
NOTICE ON INTENDED USE: 3-matic Research is intended for use as a software for computer
assisted design and engineering in the field of biomedical research.
All datasets used in this tutorial are stored in C:\Program Files\Materialise\3-matic Research 13.0
(x64)\DemoFiles or in a similar location, depending on the selected destination folder during installation.
From version 10.0 on, 3-matic Research remembers for you. This means that when opening an
operation page, previously remembered parameter values are available for further use. The below
exercises sometimes refer to the default parameter settings. In order to use these default parameter
settings, the functionality Options > Reset Current Operation Defaults can be used.
© 2018 Materialise N.V. All rights reserved.

Materialise, the Materialise logo and the Materialise Mimics and 3-matic product names are trademarks
of Materialise NV.
Tutorial 3-matic Research 13.0 5/2018, L-10788 Revision 1

/ Chapter 1: Import
Exercise 1. Import STLs
1. Open a new 3-matic Research project.
Click on Import Part, select the STLs of the aorta (Aorta1 and Aorta2) and import them
together. During import, Split surfaces with an angle of 45°. This will make separate surfaces
of all inlets and outlets.
They are positioned on the same location, since they originate from the same dataset. No
registration is necessary.

Exercise 2. Import a Mimics project file

1. Open 3-matic Research. In the File menu, select Import Part and browse to C:\Program
Files\Materialise\3-matic Research 13.0 (x64)\DemoFiles\FinishedFemur.mcs. The 3D
objects are loaded into your 3-matic Research project.
Exercise 3. Import a CAD file of a heart valve

In case you want to combine the STL model of the aorta with a heart valve design from a CAD package,
you can import the IGES file of this valve. The valve used in this exercise is NOT a real heart valve; it is
redesigned to resemble a common valve.
The IGES file is triangulated upon import.
1. Go to File – Import Part (Ctrl + L) and browse for ‘heart valve.igs’ file.
2. In the Import dialog, enable Fix normals and Stitch automatic.

/ Chapter 2: Basic
Exercise 1: Align the heart valve with the aorta
When importing heart valve.igs, the valve will not be positioned correctly yet and needs to be aligned to
the aorta. Use the STL file Aorta1 for this exercise.
1. Go to Align and choose Arc to Arc Align.
2. Fit an Arc on the aorta inlet as the fixed entity. Fit another Arc on the outer surface of the
heart valve as the moving entity. Make sure the arrows are aligned properly, to fit the heart
valve in the right direction.
3. Choose Coincident or Coincident face to face, depending on the direction of the arrows.
4. Use Interactive Translate to fine-tune the positioning if necessary. Select the Object
coordinate system to translate.
Now we need to virtually attach the aorta to the valve. Therefore, we will modify the aorta inlet to fit on
the heart valve.
5. Go to the Fix tab and choose Project Mesh. Select the inlet surface as entity. Method
is On Selection. As target entity select the outer surface of the valve.

6. Apply and the result should look like this:
7. To open the inlet, delete or hide the surface.
If you want to prepare this assembly for CFD analysis, the valve still needs to be remeshed and the
nodes should match the connecting nodes on the aorta.

/ Chapter 3: Analyze
Exercise 1. Wall Thickness Analysis
To analyze the thickness of the cortical bone, you can run a wall thickness analysis.
1. Import FinishedFemur.mcs. Make sure only the Cortical part is shown in the Work Area.
In the Analyze tab, click on the Create Wall Thickness Analysis button and select Cortical
as Entity. Set the Maximum Wall Thickness to 10.0 mm. A histogram with the wall thickness
distribution will be displayed and a range of colors will be visualized on the Cortical 3D object.
The green color represents the thinner structures, while the red color corresponds to the thicker
regions. Feel free to play with the slider thresholds for better visualization.
2. Try to Measure the wall thickness locally.
3. Go to the Export options under the File menu and select Analysis to export the created wall
thickness analysis. Choose the Cortical [Wall Thickness Analysis] from the Object Tree as
Entities and click on Output Directory to choose the folder where the analysis will be
exported.
4. The wall thickness analysis results will be saved in a text file on the selected location.


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Exercise 2. Curvature Analysis

For the purpose of guide design it might be interesting to analyze the curvature of the bone. This exercise
also uses the FinishedFemur.mcs data.
1. Select the Create Curvature Analysis button and select the Femur. Choose Maximum
curvature as Analysis Type, Noisy as Mesh Type and set the Fitting radius to 6.0 mm. Apply
the operation.
A histogram with the curvature distribution is displayed and the 3D object is represented in
a range of colors. The blue color represents the regions with local convexity, while the red
color corresponds to areas of concavity.
2. Try to Measure the Analysis Locally.

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Exercise 3. Part Comparison Analysis

1. Import Aorta1 and Aorta2 from the Demo Files and Split surfaces with 45° (refer to Chapter
1: Import – Exercise 1)
2. Go to the Analyze tab to Create a Part Comparison Analysis to compare the aorta at
systole (Aorta2) with the aorta at diastole (Aorta1).
3. Set the Histogram range from -3 mm to 3 mm.

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4. Try to Measure the Analysis Locally.
5. Select Segmentation under the Analyze menu to segment the analysis results in the defined
range. The following operation will be opened.
6. Choose Entity as Aorta2 [Part Comparison Analysis].
7. Select Histogram range between -3.0000 and 3.0000.
8. Choose other parameters as shown in the image above and press Apply.
9. The surfaces of the object are separated according to the ranges defined during the
Segmentation operation. Use the Show/Hide option to visualize the respective surfaces.
The Segmentation operation can be used in a similar way for segmenting the other analyses.

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Exercise 4. Measure and analyze using fitted primitives
1. Click on the Rectangular Mark button in the Mark tab and select the femur head of the
Femur object. To make sure that the triangles are marked through the femur head, hold the
SHIFT button whilst selecting the femur head.
2. In the Analyze (or Design) tab, select the Create Analytical Sphere function.
3. Click on Mark > Unmark All.
4. Click on the Rectangular Mark button in the Mark tab and select the femur shaft of the
Femur object. Hold the SHIFT button to mark the triangles through the object.

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5. In the Analyze (or Design) tab, select the Create Line function. Choose the Fit ruled
surface direction as the Method and the marked triangles as Fitting entities.
6. Make the resulting line longer, by using the Edit Axis function in the Analyze or Design
tab.
7. Click on Mark > Unmark All.

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8. Mark the femur neck using the Rectangular Mark tool. Make sure you hold the SHIFT
button when you mark the rectangle in the neck.
9. In the Analyze (or Design) tab, select the Create Line function . Choose the Fit ruled
surface direction as the Method and the marked triangles as Fitting entities.
10. Measure the angle using the Angle measurement from the Measure toolbar. Select
the Line to line Method and indicate the two lines. Click on Apply. Hide the femur first so
that you can select the lines more easily.

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/ Chapter 4: Design
Exercise 1. Give the aorta a thickness for additive manufacturing
1. Import Aorta1 from Demo Files into 3-matic Research with Split Surfaces checked ON (45°).
2. Separate the inlet and outlet surfaces to another part, so the aorta only consists of the outer
surface.
3. Select the (Uniform) Offset from the Design toolbar. Select the Aorta part as entity and
select Solid. A thickness of 1 mm is good for building. The picture is an example of this
aorta built on an Objet machine.

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Exercise 2. Aneurysm design

To investigate the influence of aortic aneurysms with different sizes and shapes on blood flow or
pressure, it can be interesting to be able to ‘design’ different aneurysms.
1. Import Aorta2 from Demo Files. Go to the Finish tab and select Push And Pull. Set the
Push and pull distance to 5.0 mm and the Morphing diameter to 40.0 mm. Hold CTRL to
pull on a part of the surface of the descending aorta. Rotate the aorta to pull on all sides.
Here you see an example of a CFD analysis of blood pressure on a similar aorta:

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Exercise 3. Designing an acetabular cup

In this exercise we will use forward engineering to design a customized acetabular implant, using patient
data. This way, it is possible to create a perfectly fitting prosthesis which can be used in your R&D
process. In the image below you see an example of such an implant. In this exercise we will only design
one flange, but of course the method can be copied for the other flanges.
1. Import FinishedFemur.mcs (refer to Chapter 1: Import – Exercise 2)
2. First, we will make a copy of the pelvic bone, therefore select the Pelvis in the Object Tree,
right-click and from the context menu select Duplicate. To make any of the original 3D
models invisible, right-click and select Hide from the context menu.
3. We will now simplify the Pelvis_duplicate. Select the Create Curve function in the
Curve tab, choose as Curve creation method the Attached Curve option and enable Split
surfaces. Now draw a curve over the contour of the acetabulum.

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4. Select the inscribed surface and select Delete from the context menu. If it is not possible to
select the surface, make sure the curve is closed (Curve > Close Curve) and use Curve >
Split Surfaces by Curves to separate the surface first.
5. From the Design tab, select the Surface Construction tool. Create a surface based
on the created curve.

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6. We will use the Analytical Sphere we have fitted onto the femur head during the
Analyze exercise (Chapter 3 Exercise 4), as a start for the design of the acetabular cup. In
the Design tab, click on the Convert Analytical Primitive to Part button and select your
sphere.
7. To give the sphere a thickness, go to the Design tab and click on the Hollow button.
Fill in the parameters as indicated below and click on Apply.
8. To cut the hollow sphere we will create a plane. In the Design (or Analyze) tab, select
the Create Datum Plane button. Select Fit plane and select the created surface in the
Pelvis_duplicate as Fitting Entity.

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9. You can still adjust the position of the Datum Plane. In the Align tab, select the
Translate/Rotate, choose the Object coordinate system and reposition the plane to the
borders of the acetabular cavity. Make sure the plane does not intersect with the edges of
the acetabulum.
10. Cut the hollow sphere with the Datum Plane and delete the outside part. This finishes
the design of the acetabular cup. In the next steps we will add a flange to the design.
11. From the Sketch menu select New Sketch. Select Fit Plane as Method and as Fitting
Entity, select the flat surface of the sphere that resulted from the Cut operation.

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12. Import the outline of the pelvic bone into the sketch and project the contours of the
acetabular cup onto the Sketch. Go to Sketch > Import > Import References, for Projection
select both the Contours from the sphere, and for Outline select the duplicated pelvis.
13. Create a line sequence on the ischium bone. Click on the Create Line action button
in the Sketch tab and select Line sequence. Draw three line segments and press the Escape
key to finish.

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14. Add constraints to the line segments. Select the two opposite line segments and click
on the Parallel button.
15. Set a distance of 7.0 mm between the two parallel line segments.
16. Set a length of 15.0 mm for each of the two parallel line segments.
17. Select the Sketch > Add Sketch Entity > Circle Arc (3 Points). Indicate the
extremities of the line segments and the radius of the arc.

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18. Make sure each of the line segments is tangent to the arc. Select one of the parallel
line segment and the circle arc, then select Sketch > Add Constraint > Tangent.
19. We will now project the 2D flange onto the 3D surfaces. From the Curve tab select
the Project Curve tool. The Entity will be the Sketch-001 and the Target Entity will be the
Pelvis_duplicate 3D object.
We will project according to the normal of the sketch. Highlight the direction parameter, then
expand the sketch, expand the Object Coordinate System and select the Z-axis of the
Sketch. If in the preview, the direction arrows are pointing away from the pelvis, flip the
direction by clicking on the toggle direction button. Ensure to check ON the ‘Create surface
sets’ checkbox. Click on Apply to finish the operation.

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20. Merge the surfaces resulting from the projection and separate a copy of the surface to a
new part. Rename it to Flange.
NOTE: The different surfaces are easily selectable as they are separated in a surface set.
21. Move the surface (Design > Move Surface) of the Flange object over 1.0 mm to give
it a thickness.

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22. To attach the flange to the acetabular cup select the Local Boolean operation from
the Design tab. Select the flange as Entity 1 and the outer surface of the sphere as Entity
2. Using the default Local Boolean Parameters the acetabular cup and the flange will be
united.
23. We will use a predefined screw to create the fixation holes. Go to File – Import Part and
choose STL. Select screw.stl.
24. From the Align tab select Interactive Positioning. In the Work Area select the screw as
Active object and for the Coordinate system, select the Object coordinate system. You can
now drag the screw over the surface of the flange. To create multiple holes, duplicate the
screw and use the Interactive Positioning tool to position them.
25. Merge all screws by selecting them and selecting Merge from the context menu.

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26. Subtract the screws from the flange. Select the Sphere with thickness as entity and
the merged screws as Subtraction Entity. Click on Apply.

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Exercise 4: Creating a Custom Cardiovascular Benchtop Model

One growing application in the cardiovascular market is the ability to design and print a benchtop model.
Benchtop models are helpful for many applications including stent placement research and flow studies.
The following exercise will explain the steps necessary to create such a model and is summarized in
the table below.
Task Description Illustration 3-matic Research

functionality
1&2 Prepare model Local smoothing
Hollow
Trim
3. Design base and Sketch

support Extrude
Create Cylinder
Local Boolean
4. Add flange to the Import

benchtop model
Arc to Arc Align
Interactive Translate
Loft
5. Finishing touches Quick Label
Fillet

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Task 1. Clean and Optimize the Geometry
1. Import the AAA.stl file into 3-matic Research by clicking File  Import Part. The file is
located in the DemoFiles folder.
2. Smooth any rough areas on the surface of the model using the Local Smoothing tool found
under the Finish Menu. Click and drag to apply the Local Smoothing.
Task 2. Add a Thickness and Trim the Model
1. Create a shelled structure using the Hollow operation found under the Design Menu. The
vessel wall will be created at 2 mm thick. Press Apply to create the Hollow.
2. Use the Trim tool (Finish menu) to cut the ends off of the inlets and outlets of the aorta.
Create a box around the ends of the inlets and outlets and press apply to perform the Trim
Repeat this action for all the remaining in- and outlets.

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Task 3. Design Base and Supports
1. Create a New Sketch, found under the Sketch tab, using the ‘Through 1 point, parallel to
a plane’ method. The ‘Through 1 point, parallel to a plan’ option is found under the Method tab.
As the parallel plane, select the ZX-plane of the world coordinate system. Choose a point on
the posterior side of the aneurysm.
2. Translate this sketch normal to the Y-axis using the Translate function under the Align Tab.
Move the sketching plane 30 mm so it is not intersecting the anatomy at any point.

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3. Import the outline of the aorta into the sketch. This will serve as a guide to draw the profile
of the base.
4. Using Create Line Sequence in the Sketch toolbar, draw a profile of the base in the Sketch
tab. Feel free to be creative, but be sure that it completely contains the aorta profile within the
base.

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5. To give the base thickness, Extrude the sketch in both directions 3 mm (Design menu).
The result should then have a 6 mm thick base. Hide the Sketch afterwards.
6. Now, supports will be designed to attach the base to the aorta by creating and attaching
cylinders to the base and aorta (Design  Create Primitive  Create Cylinder). Use the “Expert
Mode” Option (found at the bottom of the 3-matic Research window) Extend Length to extend
the cylinders into the AAA. Use the 2 Points method to create the cylinders with one point on
the base and one point on the AAA model. The Extend Length option is used to extend the
length of the cylinder so that it fully intersects with the AAA model. Press F3 to display the filter
options which show possible point selections.

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7. Perform a Local Boolean operation (in the Design Menu) to join the base and supports.
The first entity will be the extruded supports, and the second will be the top surface of the base.
8. Use a second Local Boolean to join the supports to the model. Here the first entity is the
result of the previous Local Boolean and the second will be the outer surface of the AAA model
(click on the AAA model and choose surface).

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Task 4. Add a flange to the benchtop model
1. Import the flange STL in the project (File  Import Part  Flange). Use the default options
for the import and click OK to continue.
2. The flange must be attached to the superior side of the AAA model. To first place the flange
at the right position, Arc to Arc Align from the Align Menu can be used. Select the inner contour
of the superior end of the AAA model for Arc on fixed entity and the inner contour of the flange
(at the side of the thin band) as Arc on moving entity. To position the flange correctly, choose
Method Coincident face to face (the arrows in the arcs will help to verify how the flange will be
positioned). Press Apply.
3. The flange is now placed against the AAA model. To make a nice transition between the
AAA model and the flange, there must be a gap between the two parts to make the connection.

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With Interactive Translate (Align menu – shortcut key: T) the flange can be translated in the Z
direction (use Object coordinate system) for approximately 30 mm.
4. With the Loft operation from the Design Menu the flange can be attached to the AAA model
and will give a smooth result. In the operation page choose Type Loft with thickness using
surface and select the side surfaces of the two parts as entities. Leave the Weight 1 and 2 on
default (exact values can be different depending on the distance between the flange and model)
and select the option Merge.

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Task 5. Apply Finishing Touches and Export
1. Put a logo on the top of the vessel using Quick Label in the Finish Menu. Choose method
Drawing and Import DXF file ‘Logo_Materialise.dxf’. Adjust the scale so that the logo fits on the
vessel. Choose a Depth of 1 mm.
2. Use the Fillet tool under the Finish menu to smooth the upper contour of the base. Use a
radius of 1 mm.
3. Add any other finishing touches to the part including final Local Smoothing, found under the
Finish tab.
4. Export the model as STL file (File  Export  STL).

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Exercise 5. Design of a patient specific cranial plate

This exercise explains how to create a patient-specific cranial plate in 3-matic Research and involves 6
main steps, as outlined in the table below.
Task Description Illustration 3-matic Research

functionality
1 Prepare the skull model and Create Curve
define the outline of the gap
Create Curvature
Analysis
Edit Curve (optional)
2 Mirror the healthy geometry to Sketch

create a guiding curve (optional)
Mirror
Translate/Rotate
Interactive Translate
Interactive Rotate
Create Spline
3 Create the cranial plate with a Surface Construction

variable thickness
Variable Offset
Uniform Offset
Boolean Subtraction
4 Remove undercuts Undercut Removal
5 Finish the cranial plate by Smooth Edge

smoothing and chamfering the
edges
Chamfer Edge
6 Create suture holes Create Cylinder
Create Isocurves
2D Linear Pattern
2D to 3D Linear
Pattern

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Task 1. Indicate the outline of the gap
Before creating the outline for the cranial plate, the skull first needs to be smooth enough. A Wrap and
Smooth operation (Fix toolbar) will take care of that. A Reduce operation will be applied first, to reduce
the number of triangles, making the model easier to work with.
1. Open the Project skull.mxp.
2. Reduce (Fix menu) the number of triangles. Apply the default settings of the Reduce
feature. To visualize the triangles, the View > Shading Modes functionality can be used
(SHIFT + F3 to quickly enable the triangle edges).
3. Smooth the skull with default parameters (Fix menu).
4. Wrap the skull with the settings shown below:
Now, the outline of the gap needs to be indicated. By doing this, we can use this outline in a further
stage to fill the gap using the Surface Construction operation in the Design menu (or the Create
Cranioplasty Prosthesis in the Plate menu). Curve operations will be used to trace the outline.

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5. Select the Create Curve operation in the Curve toolbar, and make sure you select the Curve
creation method as Smooth curve, as shown in the figure below. Check the boxes for Attract
curve and Attach curve. Create a curve around the gap on the wrapped skull.
It is important to define the curve close to the defect, but in a low curvature area, so that
tangency is maintained between the skull and the implant.
Note:
To get a good curve, place the points close enough to each other in high curvature areas.
6. To assist with identifying areas of high tangency, the Analyze  Create Curvature Analysis
tool can be used. This will project a color map of the surface curvature on the skull model. This
color map can be adjusted by adapting the values of the histogram range. Curvature Analysis
is part of the Analysis module of the Mimics Innovation Suite.
The analysis can be hidden via the context menu of the analysis in the Object Tree.
7. The curve can be closed with the Close Curve Operation if the curve is not yet closed
(can be checked in Properties).

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8. When the curve is not completely according to expectations, the Edit Curve tool can be
used.
Click on a point on the curve you want to move, a green dot appears. Now you can adjust the
influence distance to limit the area in which the curve can be moved. Now, drag the green
point to the new location and choose Apply to finish the editing operation.
Task 2. Mirror the healthy geometry and create a guiding line
This step is an optional step in the creation of the cranial plate. Guiding lines can be used for the surface
construction operation to “guide” the new surface. This allows you to create a prosthesis that fits
perfectly in the skull and results in a smooth skull-prosthesis transition.
1. First a sketch will be positioned within the sagittal plane. In the Sketch toolbar, select the
New Sketch operation. Select the Midplane Method and indicate two anatomical landmark
points, such that the sketch will be positioned in the sagittal plane.
Rename the Sketch to ‘Sketch_Sagittal’. The size of the sketch can be adjusted in the
properties by changing the parameters Cell size and Cells count (e.g.100).
2. Use Translate/Rotate (shortcut: G) where necessary to adjust the positioning.

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The standard views like front, left and top can be useful during the positioning of the plane.
These views can be found in the left toolbar
3. Create a mirrored copy of the anatomy using Align  Mirror and use the created sketch as
Mirror plane. Make sure the option Copy is checked ON.
Rename the mirrored part to ‘Skull_Mirrored’
4. Use Translate/Rotate to fine tune the position of the reference (mirrored) skull.
5. Duplicate ‘Sketch_Sagittal’ and rename the entity to ‘Sketch_Coronal’.

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Rotate the Sketch plane 90°, using Align  Interactive Rotate, such that it is positioned directly
within the defect (and becomes a coronal plane). Tick the Enable snapping checkbox to have
the plane rotating in steps of 90°.
6. Move the rotated plane so that the plane vertically divides the defect in roughly two equal
parts.
7. Import information on the skull, defect curve, and mirror anatomy into the sketch. Go to
Sketch  Import References and use Sketch_Coronal as selection entity and to load the
Skull_wrapped and the Skull_Mirrored as intersection entities. Redo the operation with the
defect curve as intersection entities.

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The points indicating the intersection of the sketch with the defect curve will serve as the starting
and ending points for the guiding curve.
8. Use Sketch  Create Spline to sketch out a guiding line. The goal is to match the mirrored
skull as closely as possible, and use the imported points as beginning and ending points.
Note:
To improve the shape of the spline, select the Sketch toolbar and use the Select and drag
operation.

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Task 3. Creation of the cranial plate

1. Select the Design  Surface Construction operation, select the outline curve that was made
in the beginning as Entities and select ‘Sketch_Coronal’ as Guiding lines. Set the Triangulation
to Fine. Select Apply.
If the resulting surface consist of a sharp random triangles, the normal of the outline curve is in
the opposite direction of the surface and should be flipped. First undo the Surface Construction
operation and then select the curve from the Object Tree and click on the tool Flip Curve
from the Curve menu. Afterwards the surface can be constructed and will result in a tangent
surface.
2. When the surface is created, it is part of the skull. In the next step the surface will be moved to
a separate part. This can be done by first selecting the surface in the Work Area and clicking
the right mouse button. A context menu will appear with different options, choose here: Separate
> Move to Part > Create New. After the surface is moved to another part, rename the part to
‘Prosthesis’.
3. The next step is to give a thickness to the surface with the Variable Offset tool from the
Design menu. With this tool, you can locally indicate along the surface contour different values
for the thickness in that area. To know what the thickness should be, measurements can be
performed on the skull like in the example below (use Measure  Distance).

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Choose the parameters from the screenshot below for the Variable Offset operation. To add
contour points to set a different local thickness, select the Points field. Now in the Work Area, a
point can be placed on the contour of the surface and a local thickness can be given. Click on
Add, to add the point to the Overview list and repeat this for all the other points.
The result after this operation can be most easily visualized when the Skull and the Prosthesis
are clipped. This can be done by selecting the Standard Section – Y in the Section List in the
Object Tree. Check on Clip in the properties page and change the Position to get the right view.
Disable the clipping before continuing with the next steps.

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4. The resulting prosthesis is not final yet, as it still intersects with the skull and does not fit well
onto the defect area. To solve this, the skull needs to be subtracted from the plate. To ensure a
smooth fit, a clearance of 0.1 mm is added in this subtraction too. This can be done either
manually with the offset workflow below or via the Clearance factor in Boolean Subtraction.
Open the tool Uniform Offset from the Design Menu. Select the Skull_wrapped as the
entity and choose a 0.1 mm external offset. Be aware to check OFF the Remove original
parameter. After the operation, rename the part as Skull_Offset. If redundant shells are present
after the offset, these should be removed before continuing. This can be done by selecting the
skull with Mark Shell from the Fix menu, followed by Invert Marking to highlight the other shells.
Press delete to get rid of the loose pieces.
For the subtraction of the skull from the prosthesis, open the tool Boolean Subtraction in
the Design menu. Choose as Entity the Prosthesis and as Subtraction Entity the Skull_Offset.
Note: After the subtraction, it is possible that the prosthesis has loose pieces. These can also
be removed by the previously explained steps Mark Shell > Invert Marking > Delete.
>
After creating the prosthesis, post-processing can be done to further improve the design of the
prosthesis. Four possibilities are discussed in the following sections:
1. When a prosthesis with a large thickness is created (e.g. if a ceramic material will be used) then
the created prosthesis will have some ‘undercuts’, that block a good fitting of the prosthesis.
2. Smoothing the edge to create a smooth contour around the cranial plate surface.
3. Adding a chamfer to the edge to create a smooth bevel around the cranial plate contours.
4. Creating suture holes to allow stitching soft tissues to the implant.

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Task 4. Removing the undercuts
The fitting direction of the prosthesis is defined as the direction in which the prosthesis should be taken
in or out. Depending on this direction, the exact area of blocking material (undercuts) is determined.
This direction can be any direction, depending on the preferences of the user. In this case, we will use
a direction that corresponds with the average normal direction of the prosthesis. To obtain this average
normal direction, the surface normal of the upper surface will be selected.
1. Apply the Remove Undercut operation from the Finish menu to remove obstructing material.
The Direction will be the surface normal of the upper surface. This can be selected in the 3D
view by clicking on the surface, while the Direction parameter in the operation page is
highlighted. Select the following parameters and select Apply.
2. The result of the Remove Undercut operation has multiple surfaces on the side surface.
These can be merged by selecting the different surfaces in the Object Tree or Work Area
and choosing Merge in the context menu. Only select the side surfaces as shown on the
picture below and not the top and bottom surfaces to ensure those contours are still
available for further finishing.

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Task 5. Creating a smooth edge and chamfered edge
The Smooth and Chamfer Edge operations are found in the Finish toolbar
1. Select Smooth Edge. Select the contour of the cranial plate you want to smoothen.
Choose the Influence distance, which will be displayed by a green curve around the contour.
Apply the Smooth detail: the more detail, the finer the result, but the longer calculations will
take.
The resulting contour is smoother:
2. Select the Chamfer Edge tool. Choose the outer contour of the bottom surface of the
prosthesis. Choose a chamfering distance and apply the operation. This results in a smooth
bevel around the bottom contour as shown in the picture below:
The result can be fine-tuned by using the Trim and Local Smoothing tools of the Finish menu.

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Task 6. Creating suture holes
The last step of this exercise shows how to make suture holes that can be used to fix soft tissues to the
prosthesis.
1. First a cylinder needs to be created that will be patterned and subtracted from the
prosthesis to create holes. Go to the Design menu and choose the tool Create Cylinder. Select
a radius of 1 mm and choose Point 2 such that the length of the cylinder becomes 14 mm.
In the rest of this task, the Texturing module will be used to pattern copies of the cylinder across the
plate. After placing a texture on the surface, the pattern of this texture will be used to determine the
location of the cylinders.
2. First, the surface needs to be prepared before the pattern can be placed on the surface.
Use the Create Isocurves tool from the Texturing module. Select the contour of the outer surface
of the plate as Entity. Set the Direction to Inside and the Interval distance to 2 mm. Make sure
Split Surfaces is checked ON. Press Apply.
3. To place a texture on the plate, use the 2D Linear Pattern tool under the Texturing Module.
Select the newly created outer surface as Entity. Note the naming in your project might be
different. For educational purposes, make sure the Create UV Page is checked ON, then press
apply. Note: for this workflow no modifications in the UV page are required.

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4. Now the UV page will be shown on the right side of the Work Area. The UV Page shows
the texture in 2D and the Work Area shows the texture in 3D. In 3D, the texture will be stretched
according to the curvature of the surface. There is a dedicated UV toolbar which allows to
interactively translate, rotate and scale the texture. These dimensions can also be controlled in
the Properties page (you can e.g. change the Width and Height to 5 mm).
For our suture holes workflow the size does not matter as it will be controlled during the 2D to
3D linear pattern step by controlling the size of the cylinder object.
To exit the UV page, press the Exit button on the toolbar.
5. To pattern the cylinders on the plate, use the 2D to 3D Linear Pattern tool under the Texturing
Menu. Select the pattern from the previous step as 2D pattern and the cylinder as Pattern entity.
Set the Preferred distance to 3 mm and the Depth to 13 mm. Check the Preserve pattern entity
size and Edit 2D pattern dimensions ON, this will modify the pattern and preserve the original
size of the cylinder. Switch the Desired result to Substract results. Press the Preview button,
before pressing Apply, this is useful to inspect the result.

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With the preview confirm all the cylinders are completely perforating the plate. When everything
looks fine, press Apply.

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/ Chapter 5: Remesh
Remeshing is intended to optimize your models for FEA (Finite Element Analysis) or CFD
(Computational Fluid Dynamics) purposes. In the Mimics Innovation Suite, all 3D models are made out
of triangulated surfaces. This allows capturing very complex geometrical structures accurately. The
remesh operations enable you to quickly and easily transform badly shaped triangles into more
equilateral triangles. The more geometrically ‘regular’ the triangles are, the more accurate the results of
the FEA/CFD calculations will be.
Basic explanation of the finite element method

The intent of a finite element method is to represent an object with a limited number of elements that
are connected to each other by nodes. This allows approximating the behavior of a complex structure
with a series of partial differential equations, which are numerically solved. For example, it can be used
to calculate mechanical stresses in implants during gait.
The smaller the elements become, the more the method converges to the analytical solution, which is
often too complex to be solved by itself. However, more elements are needed when the element size is
reduced, which makes the calculation more complex and time-intensive. Choosing the correct element
size is thus very important to reduce the complexity of the analyses, but still provide sufficient accuracy
for the application. Typically, a small element size is used for small features and a bigger element size
for regions that are less of interest.
Element quality
The element types that are used in 3-matic Research are triangle surface elements and tetrahedral
volume elements. The quality of the mesh is assessed by how well the elements resemble equilateral
triangles and tetrahedrons. This quality influences the capability of the solver program to converge to a
solution and affects the accuracy of the numerical simulation. For example: badly shaped elements are
more likely to collapse when one of the nodes is moved, which will give an error in most solver programs
and stop the calculation. Sharp angles, flat angles or a distorted shape are typical indications for a bad
quality element.
The quality of the elements can be inspected in 3-matic Research with shape measures related to
triangle properties such as base, length, angle, height, etc. These shape measures indicate how much
the elements resemble an equilateral triangle or tetrahedral element. More information about the shape
measures and their specific values can be found in the Remesh chapter of the reference guide.
Good quality element Bad quality element

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Typical Remesh workflow
1. DICOM (Mimics Research)

Mimics Research allows you to segment the anatomy of interest from DICOM images.
2. 3D anatomy (Mimics Research)

From the segmented DICOM images a 3D part can be generated, which can be exported to 3-
matic Research for further pre-processing.
3. Smooth anatomy (3-matic Research)
Often parts contain little details/artefacts that are not needed for the final FEA/CFD
simulation. Representing these details requires a small triangulation, which increases the total
number of nodes. By performing the Smooth or Wrap operations, the geometry & topology of
the part can be simplified. This reduces the total number of triangles needed to represent the
part.
4. Optimized mesh (3-matic Research)

3-matic Research contains several tools to optimize the surface element quality:
 Adaptive Remesh: Optimize and locally refine the mesh while preserving detailed features.
 Uniform Remesh: Provides a uniform and high quality surface mesh.
 Gradient Remesh: Improve the growth rate between the elements.

 Quality Preserving Reduce Triangles: Reduce triangles while preserving element quality.
Once you are satisfied with the surface mesh, the “Create Volume Mesh” tool will generate
tetrahedral elements starting from the surface elements.
5. Materials (Mimics Research)
The volume mesh can be combined with the DICOM images in Mimics Research. This
allows you to assign realistic material properties to the mesh derived from the CT gray values.

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Tips and tricks

 Always undo the previous remesh, when testing out optimal meshing parameters.
 Before creating a volume mesh, it is a good idea to check for intersecting triangles with the
Fix Wizard of the Fix menu. Intersecting triangles will not allow creating a volume mesh.
 Performing a smooth after a remesh operation can further improve the mesh quality.
 When setting a maximum edge length for the Volume it is advised to minimally use an edge
length that is slightly bigger than the surface edge length.
 In the properties of the Volume List, you can change the visualization of the volume elements
to make the edges more visible.
 The Manual Surface Mesh Tools allow you to refine single elements. For most of these tools,
holding Ctrl allows for more user control of the element refinement.
 Uniform Remesh tool
o Autofix:
Autofix, expert mode option, will solve typical surface problems this algorithm
encounters. E.g. noise shells, inverted triangles, overlapping triangles, intersecting
triangles, etc. For most cases this works fine, but if you notice that relevant shells are
removed it is advised to turn the Autofix off and perform the fixing manually.
Original Without Autofix With Autofix (default)
o Slivers:
When your part has sliver triangles, it is advised to pre-process the mesh or area, by
remeshing the part with the Adaptive Remesh tool. Alternatively you can use multiple
iterations of the Uniform Remesh, but this can increase the geometrical error.
Original Without Pre-processing With Pre-processing

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Exercise 1. Introduction to the workflow

This exercise will guide you through a typical FEA workflow, starting from the 3D part in Mimics Research
to a quality volume mesh with material properties based on the medical images.
Task 1. Import and visualize the mesh
1. Open Mimics Research. Go to File > Open project and browse to “C:\Program
Files\Materialise\3-matic Research 13.0 (x64)\DemoFiles” and open Femur.mcs. Copy the
3D object “Yellow2” to your clipboard.
2. Open 3-matic Research and press CTRL + V to paste the part into 3-matic Research.
3. In the Object Tree change the name to “Femur”. Select the femur and go to the Properties
page. This provides information about the number of triangles and nodes (Points).
Optional: change the color of the Front face to a more bone-like color (Red: 255, Green:
240, Blue:206).
4. Change the view from Smooth Shaded to Filled with Triangle Edges [Shift + F3].

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Task 2. Reduce the details of the anatomical part

1. Reduce the amount of detail in the femur. Click on the Smooth button in the Fix tab and
apply the default parameters. Alternatively, the Wrap option in the Fix tab can be used.
A smooth surface makes it easier to represent the geometry with a larger element size, which reduces
the computational cost for the solver program.
Task 3. Remesh the surface elements

1. Optimize the surface elements with the Uniform Remesh tool. Adjust the parameters as
shown below and apply the operation.
When changing the Target triangle edge length, the logger will provide an estimation of the number of
triangles that will be generated and the memory usage.
Task 4. Generate the volume mesh

1. In the Remesh tab, select the Create Volume Mesh button. To have a uniform mesh
inside the model define the Maximum edge length typically slightly bigger than the maximum
edge length of the surface mesh. For now use 3 mm and Tet4 elements.

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Setting a maximum edge length may increase the number of elements, which will cause an increase of
calculation time in the solver program.
2. To visualize the effect of the volume generation go to the Work Area and clip the 3D objects
using the Standard Section – Y as a clipping plane and adjusting its position.
Task 5. Material assignment

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CT scans of bones can be used to assign material properties to the FEA model, since there is usually a
direct relation between the intensity of the images (Hounsfield unit or gray values) and the density of the
bone as depicted in the schematic below. By combining the information of the DICOM images and the
volume mesh an accurate material assignment can be performed in Mimics Research.
1. In 3-matic Research, select and copy (Ctrl+C) the volume meshes of the “Femur”. Go back to
Mimics Research, where the original project was open, and press Ctrl+V to paste the volume
meshes. The volume mesh will appear in the FEA Mesh Project Management tab, on the right-
hand side of the Mimics Research interface.
2. With the Materials Tool, under the FEA Mesh Project Management tab, the material
properties (density, Young’s modulus and Poisson’s ratio) can be assigned. Make sure the
Femur is selected and then click on the Materials tool. The Material Assignment dialogue box
will then pop up.
A gray-value based method will be used for the material assignment. More precisely, two
material types will be defined:

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- Material type 1: One material value with a density of 50 kg/m^3 will be used for all negative HU
values until 100 HU. The purpose of this material type is to set a lower limit for the density and
it helps to prevent negative density values.
- Material type 2: Ten materials will be used to cover the trabecular bone and cortical bone range.
Let’s take 50 kg/m^3 and 1900 kg/m^3 as the minimum and maximum density values of the
bone.
For both material types we will use the following Young’s modulus (E) and Poisson ratio (v):
E = 0.004*ρ^2.01 (MPa) and v=0.3.
The Mimics Research reference guide contains Empirical Expressions for several bone types with
references to the corresponding papers.
(Mimics Menus > FEA/CFD> Assign Material> Material Expressions > Empirical expressions)
3. Start by creating an additional tab by pressing on the [+] button next to Material type 1.

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4. For material type 1 use the following settings:
5. For material type 2 use the settings below. Afterwards press “Apply” and “Close” the window.

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6. To inspect the inside of the model use the clipping functionality. Make sure the Texturing
is on None.
7. Finally you can export the mesh with material properties to a solver program. File > Export.

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Exercise 2. Inspect mesh quality

In this exercise you will learn how to inspect the quality of the surface and volume elements. Also, it will
be shown how the Smooth operation can further improve the results of the Adaptive Remesh tool.
1. File > Open Project > DemoFiles > Heart.mxp
2. The Fix Wizard of the Fix menu allows inspecting and solving overlapping and
intersecting triangles, which are often present in thin complex structures. By pressing Follow
advice, the Fix Wizard can solve most problems automatically.
Do not use the Follow advice option when dealing with a Non-manifold Assembly.
Task 1. Inspect the quality of the surface mesh
1. To inspect the properties of the mesh, open an Inspection View by selecting the
object in the Object Tree and clicking on the Inspect Part button in the Remesh tab. With
this view, different quality parameters of the surface mesh can be investigated and
elements with bad quality can easily be located. Note that the values shown in the
screenshots can be different between users.
Shape measure: Way of comparing the shape of the elements with an equilateral triangle
Inspection measure: Inspect a property of the elements e.g. height, edge length, angles, etc.
Growth measure: Inspect the transition from smaller to larger triangles

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2. In the Quality parameters section, adjust the Shape measure to Skewness (N) and in
Histogram parameters make sure that Current measure is set to Shape measure. Adjust
the Maximum number to 0.3, by typing or dragging the green outer edge of the histogram.
The histogram shows that a certain percentage of the triangles have a shape quality lower
than 0.3, in this case 16%. This value can also differ from user to user.
3. To visualize the triangles with a quality lower than the specified threshold, select the Color
low quality triangles checkbox. The colors of the triangles correspond to the colors of the
bars in the histogram.
Task 2. Remesh the surface elements
1. To optimize the surface mesh the Adaptive Remesh is used. Adjust the parameters as
shown below and apply the operation. Check the influence of the Adaptive Remesh
operation on the Inspection page.

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Task 3. Further improve the mesh by Smoothing

1. Go to the Fix menu and select the Smooth tool. Make sure to use the smooth on
separate Surface sets to preserve the edges of the in- and outlets.
2. Inspect the effect of the smoothing on the histogram of the Inspection Page.
3. Redo the Adaptive Remesh with same parameters as before to further optimize the
mesh and fix issues that might have occurred in thin regions.

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Task 4. Generate a Tet10 volume mesh
For this example a Tet10 tetrahedron will be created, which has an extra node in the middle of each
connection. Tet10 elements are commonly known as quadratic tetrahedron elements and make it
possible to simulate non-linear element behavior, as shown below.
Tet4 element Tet10 element Non-linear behavior
Non-linear element behavior can provide more realistic results, but is more difficult and computationally
intensive to calculate.
1. Use the Create Volume Mesh tool and select Tet10 as the element type. Afterwards, check
the logger information, it will provide feedback on the quality of the mesh depending on the
values set in the Analyze mesh quality section.
With the expert mode you can project the mid nodes on the original (not remeshed) surface.
Original shape (not remeshed) Tet10 of remeshed shape Tet10 with projected midpoints

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Task 5. Inspect the quality of the volume mesh
1. Open the Analyze Mesh Quality tool in the Remesh menu. This tool allows you to
inspect the quality of the surface and volume mesh.
2. Check the Display the shape measure list checkbox and switch between the solvers to see
the effect of the solver setting. Afterwards you can uncheck the list.
3. For now use Custom as a solver. Press Apply and check the logger information. As you can
see the mesh passed all the criteria.
4. If you want a more detailed overview of a certain shape measure you can plot a histogram.
Check Calculate histogram, put it on Volume and change the Shape measure to Aspect
ratio (A). To find the location of a bad element use the Mark bad elements box. Put the
parameter values as shown below and press Apply. The logger information will display the
mesh statistics and the 3D view will show the triangles that do not reach the shape quality.

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Exercise 3. Local mesh refinement

To reduce the computational cost of running a FE simulation without compromising the quality of the
results, it is often desired to have a large density of elements in a certain area while having a lower
density of elements in other areas.
Task 1. Surface refinement

1. Go to File > Open Project > DemoFiles > Femur.mxp
2. Use the Rectangular Mark tool to select part of the femur head (Mark menu). Make sure to
hold the SHIFT button when making the selection. Create a new surface, as shown below.
Afterwards, do the same for the lower extremity of the femur. Make sure to rename the surfaces,
with an appropriate name.
3. Open the Adaptive Remesh tool and use the Adaptive Remesh parameters as shown below.
For the Local remesh parameters do the following: use the head as the entity and set the
Maximum edge length on 1 mm and use an Influence area of 0 mm, then press Add. Next
remove the head as an entity, by pressing delete, and now select the bottom as the entity. Now
use a Maximum edge length of 2 mm and an Influence area of 0 mm, press Add again. Change
the Growth rate to 10 and press Apply.
The influence area allows you to expand the area, where the defined local Maximum edge length will
be used, with a distance in mm. This is particularly useful when using contours as entities for local
remeshing.

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4. Perform a smooth operation to further optimize the mesh. Go to Fix > Smooth .
You can use a variety of input entities for the local remesh parameters: curves, surfaces, parts, etc.
These entities do not need to belong to your part e.g. using an additional sphere part:

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Task 2. Volume refinement
1. Next, we will create the volume mesh, using the same parameters as for the surface mesh.
Go to Remesh > Create Volume Mesh, the same Local volume mesh parameters as for the
surface mesh will be used.
When using a surface as a local entity, the elements will grow towards the inside with the defined growth
rate. When using a Part as a local entity all the elements inside that part will have the defined local edge
length.
Using a surface Using a part
2. Clip the part to visualize the inside. You can see the volumes are gradually growing from the
surface to the middle.
3. In the properties of the Volume List, you can change the visualization of the volume elements
to make the element edges more visible.

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Exercise 4. Gradient Remesh

The Gradient Remesh tool allows you to create a smooth transition between small and large triangles.
The smooth transition is either based on the area of the triangle (called Area-growth) or on the largest
edge length of the triangle (called Edge-growth). The range of the transition area is based on a ring
definition, which decides which neighboring elements have to be considered to determine the smooth
transition, as illustrated:
1. File > Open Project > DemoFiles > Aorta.mxp
2. Use the Adaptive Remesh to provide the wall with an edge length of 4 mm and the In-outlets
an edge length of 1 mm. Notice the bad growth rate between the wall and the in-outlets.
3. Click on Aorta in the Object Tree and use the Inspect Part tool. In the Quality parameters
set the Growth measure on Edge-growth 3-rings and change the Current measure to Growth
measure in the Histogram parameters. Put the maximum of the histogram on 0.5, we will use
this as a reference.

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4. Open the Remesh > Gradient Remesh tool and use the following parameters to improve
the growth:

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Exercise 5. Creating a Midplane mesh

A mid-plane mesh is typically used to represent a solid model by a single surface. To approximate the
volume a thickness property has to be assigned in the solver program. Midplanes are particulary useful
for representing thin geometries, these would otherwise require a fine mesh to accurately represent
bending behavior.
1. Open Project Aorta_Hollow.mxp from the demo files.
2. Use the right mouse button in the object tree to copy the Outer Wall surface and Inner Wall
surface to a new part. Rename the respective parts as “Outer Wall” and “Inner Wall”.
3. For creating a midplane, go to Remesh menu and select the option Create Midplane.
Select Entity 1 as Outer Wall and Entity 2 as Inner Wall. Click on Apply to perform the
operation.
4. After the midplane is created, go to Remesh menu and select Adaptive Remesh. Select
Entities as midplane, Target triangle edge length parameter as 1.0 mm and check ON
Preserve surface contours. Click on Apply to perform the operation.

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5. To analyze the width of the midplane go to Analyze menu and click Create Midplane
Thickness Analysis. Select Entity as midplane and Limiting Entities as Outer Wall and Inner
Wall. Click on Apply to perform the operation. The histogram result shows that the width of the
midplane is approximately 1.0 mm. For this part we know the width of the wall was 1 mm, but if
you have a more difficult part with an uneven thickness a similar analysis needs to be performed.
6. Export the surface mesh of this model and assign a thickness of 1 mm in the solver program.

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Non-manifold Assembly
Performing loading simulations on a bone-implant interface is interesting for several reasons, e.g. in
order to check whether the loads are properly transferred from the plate to the bone.
Since non-conforming surfaces generally tend to create high stress concentrations, thus resulting in an
unrealistic loading situation, it is quite important for a Finite Element program that the meshes of both
the plate and the bone have shared nodes at the interface.
The Mimics Innovation Suite can solve this problem by creating a non-manifold assembly. This tool
allows assembling two or more parts into one combined part, which has a shared surface at the
intersecting regions. Now the parts can be remeshed thereby ensuring a good interface between the
parts. The parts can be split after the remesh, this will create parts that have matching nodes at the
interface surfaces.
There are three possibilities that allow generating a non-manifold assembly.
1. Mimics Research:
Mimics Research can convert masks to a 3D non-manifold part. Use this method when
there is a mask of each part available.
2. 3-matic Research (Intersection-based):

3-matic Research can generate a non-manifold part based on a Boolean operation. Use
this method when not all the parts have a mask available and when the parts are intersecting
with each other.
3. 3-matic Research (Grid-based):

3-matic Research can generate a non-manifold similar to Mimics Research by converting
the parts to a specified grid. Use this method when not all the parts have images available
and parts do not have proper intersections.
Do not use Fix > Fix Wizard for automatic fixing of the non-manifold part. The Wizard will try to fix
features that are typical for a non-manifold assembly. The tool can still be used for diagnostics.

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Exercise 6. Creating Non-manifold Assembly for anatomical parts

In this exercise you will learn how to make an assembly with Mimics Research. All parts of interest have
a segmented mask and there is no need to add a CAD part, so an assembly with Mimics Research will
be the best approach.
Task 1. Generate Non-manifold Assembly in Mimics Research
1. Open project “Spine.mcs” in Mimics Research.
2. Go to the Masks tab under the project management tab, mark the assemblies in the list by
clicking on in the following order L4 > L3 > Disc_L3_L4. The order is important, the first
selected mask will be subtracted from the ones which are selected later.
3. Go to FEA/CFD in the menu and click on Calculate Non-manifold.
4. Use the parameters as shown in the figure below and click on Calculate.
The quality of the resulting mesh is better when using a cube-like matrix, however, this affects the
accuracy of the resulting mesh.
5. Copy the generated assembly of the vertebral column to your clipboard by selecting the
assembly and pressing Ctrl+C. Open 3-matic Research and paste the part.

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Task 2. Reduce details and Remesh the surface elements
1. After the assembly is present in 3-matic Research, press [Shift + F3] to visualize the
triangulation on the assembly.
2. Reduce the amount of detail in the vertebral column. Go to Fix menu and select Smooth or
use the shortcut [Alt+S], select Assembly as Entity, use 0.7 as Smooth factor, check OFF the
Perform post processing option and click on Apply.
3. Upon a quick inspection of the properties and mesh quality, the quality seems sufficient
and we only have to reduce the number of triangles. With Inspect Part you can determine the
current edge length and current quality of the triangles: average edge length of 1 mm and quality
over 0.5 for skewness.
4. To reduce the triangles of the Assembly while preserving their quality go to Remesh menu
and select Quality Preserving Reduce Triangles. Use the parameters as shown in the image
below and click Apply.

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5. Optional: Use Smooth and Adaptive Remesh operations in sequence to further optimize
the quality of the mesh of the vertebral column. Use the Smooth and Adaptive Remesh
parameters as shown in the images below and click Apply.
When using the Uniform Remesh tool, the smooth curve operation can help to improve the interface
contours. Go to Curve > Smooth Curve, select the bad contours and press Apply.

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Task 3. Create volume mesh
To introduce a slight element growth internally in your model you can use the Local volume mesh
parameters and define only an edge length of 2 mm around the surface.
1. Go to Remesh > Create Volume Mesh, select Assembly as Entity. Select the surfaces of
the assembly as Entities for Local volume mesh parameters. Set the parameters as shown
below, click on Add and then press Apply.
2. Use the Standard section – Y to Clip the volume mesh.
Task 4. Material assignment
1. In 3-matic Research, select and copy (Ctrl+C) the volume meshes of the “Vertebra”. Go back
to Mimics Research, where the original project was open, and press Ctrl+V to paste the volume
meshes.
2. Rename the sub-volumes to avoid confusion, hide the sub volumes one by one to figure the
order out.
3. Assign the material properties on the subvolumes, with the Assign Material tool.
For the Vertebrae use gray value based method and the following expressions:

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ρ = 47 + 1.122* HU [kg/m3]
E = 0.02 *ρ^1.75 [MPa]
V = 0.3
For the Intermediate Disc use a homogenous material assignment. You do not have to wait for
the histogram to be calculated, since it is only one value.
ρ = 1000 [kg/m3]
E = 4.2 [MPa]
V = 0.45
4. Use clipping to internally inspect the part.

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5. Finally you can export the mesh with material properties to a solver program. Go to File > Export.

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Exercise 7. Creating Non-manifold Assembly for intersecting parts

In this exercise you will learn how to make an assembly with 3-matic Research. This is an example for
when there are for some parts no images available and they are intersecting or can be easily modified
to be intersecting. For these cases the intersection-based method provides the most accurate results.
1. File > Open Project > DemoFiles > BonePlate.mxp
2. The interface between the bone and the plate can be better visualized by changing the
transparency level of the bone; in order to do this, right-click on the Bone in the Object tree and
choose Transparency  High. Set the transparency for the Plate on medium.
3. You will notice that the plate does not intersect with the bone. To make this intersection use
Move Surface tool in the Design menu. Select the bottom surface of the plate and apply the
following settings. If you do not have the Design menu available you can continue with the
hidden part: Plate_MovedSurface.
4. A recommended step when creating a Non-manifold with this method is to first remesh all
the surfaces with similar parameters. Go to Remesh > Adaptive Remesh and use the following
parameters:

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5. Select the Create Non-manifold Assembly from the Remesh menu. The main entity is the
object whose volume will be reduced with the inserting entities. The volume of the intersecting
entity will be preserved. The order is important, the bottom ones will always be subtracted from
the top entities.
6. Hide the original parts in the object tree.
7. The Create Non-manifold Assembly tool generates different surface sets respectively
corresponding to the main entity (Plate), the intersecting entity (Bone and screws) and the
interface between them. Show/hide each of the surface set separately to see how the Boolean
operation of the non-manifold was performed.
8. Now improve the mesh between the parts with Adaptive Remesh. Use the parameters as
mentioned in the image below. Make sure the expert mode is ON.

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9. The next step is to split the Non-manifold back into separate parts. Use Remesh > Split
Non-manifold Assembly tool and select the assembly as Entity and press Apply.
10. The final step is creating a volume mesh of each part. Go to Remesh > Create Volume
Mesh. Use a similar maximum edge length as used for the surface mesh, 0.5 mm.

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Exercise 8. Creating a Non-manifold Assembly with a grid

In this exercise you will learn how to make an assembly with 3-matic Research. This is an example for
when there are for some parts no images available and the parts are difficult to modify to be intersecting.
For these cases the grid-based method provides the best results.
Task 1. Creating the non-manifold assembly
1. Open project Composite.mxp from DemoFiles
2. To create the non-manifold assembly go to Remesh > Create Non-manifold Assembly. Use
the grid-based method and set the parameters as shown in the image below.
The smaller the grid size the more accurately the non-manifold will represent the original parts, but this
will increase the computational efforts (see logger information).
Task 2. Reducing the number of triangles

The grid-based method will already provide good quality triangles, but depending on the grid resolution
a high number of triangles can be generated. With 3-matic Research you can keep a high number of
triangles at the interface contours and reduce the triangles in the other areas.

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1. In the object tree, convert the bad contours to curves and group the curves together in a curve
set.
2. Go to Remesh > Adaptive Remesh. Make sure the Expert mode is ON. To reduce the
number of triangles, use the parameters as shown in the image below.
3. Delete the curve set from the part, this is no longer necessary.
4. Use the Smooth operation on the different surface sets to improve the quality. Go to Fix ->
Smooth and use the parameters as shown in the image below.
5. Go to Remesh > Split Non-manifold Assembly and use the parameters as shown in the
image below.

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Exercise 9. Improving the accuracy of the grid-based method

Conversion to a grid will always cause some geometrical errors. For CAD parts these errors can be
higher than desired. 3-matic Research can regain accuracy, by projecting the surfaces back on the
original mesh. In this exercise it is shown how you can perfom this projection and how to identify and fix
intersecting triangles caused by the projection.
Task 1. Creating the non-manifold assembly
1. Open Project Trabecular_Screw.mxp from DemoFiles.
2. To create the non-manifold assembly go to Remesh > Create Non-manifold Assembly and
use the parameters as shown in the image below.

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Task 2. Improving the accuracy of the screw
3. Hide the Trabecular surface set and visually compare the original screw with the screw in the
assembly.
4. To improve the accuracy of the screw go to Fix > Project Mesh. For Entities use the screw
surfaces sets of the assembly. For Target entity use the original screw and make sure the
method is On selection.
Task 3. Dealing with intersecting triangles

The projecting step might introduce intersecting triangles. Note that when using a small grid size there
is less chance of intersecting triangles.
1. Use the fix wizard to identify the number of intersecting triangles.

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2. You can single out islands of the intersecting areas to easily identify and fix the intersecting
areas. Make the trabecular surface visible and use the following tools in this order to create
those islands:
a. Fix > Mark Intersecting Triangles or press [Shift + Q] (make sure the part is selected)
b. Mark > Expand > Expand by Number
c. Mark > Invert or press [F9]

d. Mark > Make Invisible or press [H]
e. Fix > Mark Intersecting Triangles or press [Shift + Q]

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3. Use the manual surface mesh tools to fix the area.
a. Use Delete Triangle to delete the intersecting triangles. Often some neighboring
triangles have to be removed as well.
b. Use Create Triangle to fill up the hole. Make sure the nodes are properly connected.
4. Mark > Make All Visible
Task 4. Improving the mesh

Triangles of the trabecular structure, which are located at the interface, are elongated with the projection
of the screw. Because the rest of the mesh has still a good quality only this area will be remeshed.
1. Create a curve from all the Bad Contours by [Right Mouse Click] > Separate > Copy to New
Curve. Group all the Curves in a new Curve Set by [Right Mouse Click] > Separate > Move to
New Curve Set
2. Mark > Mark Entities, select the curve set. Press the up arrow or Mark > Expand >
Expand

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3. Use the Adaptive Remesh on the marked areas. Use a Target edge length with a value
slightly smaller than the grid size that was used during the assembly.
4. Right click and Unmark All
5. Delete the Curve Set in the Object tree.
Task 5. Creating volume mesh and identifying bad volume elements

1. Create a volume mesh with the parameters as shown in the image below. Notice in the
logger, there is one bad volume element.

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2. Analyze the mesh quality, go to Remesh > Analyze Mesh Quality . Use the parameters as
shown in the image below.
3. Hide the Volume List and identify the bad elements, by making islands.
a. Mark > Expand > Expand by Number
b. Mark > Invert or press [F9]

c. Mark > Make Invisible or press [H]
4. Notice that the bad volume element is created in an area with overlapping triangles. Use the
manual surface mesh tools to fix this area.
a. Use Delete Triangle to delete the overlapping triangles. Often some neighboring
triangles have to be removed as well.
b. Use Create Triangle to fill up the hole. Make sure the nodes are properly connected.
5. Make all visible again and regenerate the volume mesh . You will notice that the quality
has improved.

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6. Split the non-manifold assembly with the Automatic volume method.

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Exercise 10. Exporting and importing the mesh into a solver

program
Task 1. Generating a mesh with material properties
1. Open Mimics Research. Go to File > Open project and browse to “C:\Program
Files\Materialise\3-matic Research 13.0 (x64)\DemoFiles” and open Femur.mcs. Copy the
STLs “Femur” and “Implant” to your clipboard.
2. Open 3-matic Research and press CTRL + V to paste the parts in 3-matic Research.
3. Go to Remesh > Create Non-manifold Assembly to create a matching node interface.
4. Use Adaptive Remesh to improve the surface mesh, go to Remesh > Adaptive Remesh.

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5. Improve the surface mesh by performing a smooth on each surface separately. Go to

Fix > Smooth.
6. Go to Mark > Brush Mark > Wave Brush Mark or press [M]. Use a diameter of 20 and
mark the implant head to simulate the area of contact. Separate the area and rename the
surface to “Contact”.
7. Rename the bottom surface to “Fixed’.
8. To generate a volume mesh go to Remesh > Create Volume Mesh.

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9. In 3-matic Research, select and copy (Ctrl+C) the assembly. Go back to Mimics Research,
where the original project was open, and press Ctrl+V to paste the volume meshes in the
Mimics Research project.
10. Rename the subvolumes to avoid confusion, it can help to hide the subvolumes one by one.
11. Go to FEA/CFD > Assign Material and select the Femur subvolume and assign the
following material properties:

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12. Select the Implant subvolume and assign it the following homogeneous material properties:
ρ = 4500 [kg/m3]
E = 55000 [MPa]
V = 0.33
For this exercise ANSYS will be used as a solver program. You can find short instructions on how to
import the mesh in other solver programs below.
Task 2. Exporting the mesh to ANSYS® Workbench™
1. Go to File > Export > Ansys, select the part and press Add. Set ANSYS as the output format.
Select the Output file and press Edit and add the surface structure. Press OK to export the part.
2. Open ANSYS® WorkbenchTM

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3. Drag the “External Model” component and “Static Structural” analysis to the Project Schematic.
4. Open External Model, with a double click on the Setup. Browse for the .cdb file generated by
Mimics Research. Make sure to put the units in mm.
5. Drag the Setup from the external component to Model of the Static Structural analysis. Then
update the project.
6. Double click on Model of the Static Structural analysis to open the analysis.
7. Open up the contact Region and change the contact definition from Bonded to Frictional and
use a Friction coefficient of 0.6.

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8. To assign the material properties right click on the Static Structural and insert a command. Right
click on the Command and Import the .txt file that was exported by Mimics Research.
9. Add a Fixed Support at the bottom of the femur.
10. Add a force of 2800 N in the -Z direction on the contact surface of the implant.
11. Use the equivalent (von-Mises) stress for the solution and press “Solve” .

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Exporting a file to ANSYS® Workbench™ version 14.0 or earlier
1. Open ANSYS® WorkbenchTM
2. Drag the “Finite Element Modeler” component and “Static Structural” analysis to the Project
Schematic.
3. Right click on Model from the Finite Element Modeler > Add input mesh > Browse… Make sure
your input is on Mechanical APDL input (*.cdb). and select the file generated by the Mimics
Innovation suite.
The ANSYS® Finite Element Modeler can also read ABAQUS Input (*.inp) files and for this file format it
manages to use the surfaces as named selections.
4. Drag the Setup from the external component to Model of the Static Structural analysis. Then
update the project.
5. Adding the material properties is similar as explained above.
Exporting a file to ABAQUS/CAETM

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1. When exporting an assembly to ABAQUSTM it is recommended to first split the assembly

with the Split Non-manifold Assembly tool.
2. During the export, File > Export > ABAQUS, you can group the parts in one .inp file (example
3-matic Research).
3. Open Abaqus/CAETM . Create a new database.
4. File > Import > Model… Make sure the file filter is on Abaqus Input File (*.inp, *.pes) and
select the file that was generated by the Mimics Innovation Suite.
Exporting a file to COMSOL Multiphysics®
1. File > Export > COMSOL, if you want to export the surface boundaries to COMSOL
Multiphysics®, it is recommended to export both the surface and volume mesh (example 3-matic
Research).
2. Open COMSOL Multiphysics®.
3. Create a new model by using the “Model Wizard”.
4. Select “3D” as Space Dimension.
5. Select the Physics (e.g. select “Solid Mechanics (solid)” in the “Structural Mechanics” module)
and click Add. Continue by clicking Study.
6. Select the Study (e.g. Select Stationary ( )) and click Done.
7. In the Model Tree click “Geometry” and select “mm” as Length unit.
8. From the menu select the “Mesh” tab and click “Import”. Via the file browser navigate to
the .mphtxt file generated by the Mimics Innovation Suite. Click “Open” and click “Import” to
start the import process.

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Exporting a file to MSC Patran®
1. In 3-matic Research go to File > Export > Patran or Nastran (example 3-matic Research).
2. Open MSC Patran®.
3. File > Import…

Set Object to Model.
Set Source to Neutral (.out) or MD Natran Input (.nas, .bdf).
Select the file generated by 3-matic Research and press Apply.

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/ Chapter 6: Texturing
Introduction to the Texturing module

The Texturing module offers the possibility to apply 2D/ 3D textures on a surface. This will be done
based on a picture (*.Jpeg, *.Bmp or *.png).
The first step of applying a texture is wrapping the bitmap on a surface. The second step will give an
offset to every pixel of the picture. This offset-value is depending on the black/ grey/ white color in the
picture.
The first picture above shows a part with the picture applied to the surface. The second picture shows
the 3D picture created, based on the picture.
Exercise 1: Applying a Texture to an Imported STL

Task 1. Import the file
1. Open 3-matic Research and select the File menu, select ‘Import Part’, select the Shoehorn.STL
2. Make sure the option ‘split surfaces’ is checked OFF, Select ‘OK’.
The part is imported in 3-matic Research and visualized in the Work Area.
Task 2. Create a surface for texturing

The texture will be created on the front of the shoehorn. First a surface will be created on the front of
shoehorn.
1. Select the Mark Toolbar > select the ‘Mark Smooth Region’ operation > Mark the front of the
shoehorn > Right-click on the marked triangles > Separate > Move to Surface > Create New.

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To create a small edge without texture, an offset will be given to the contour line.
2. Select the Texturing toolbar > select the ‘Create Isocurves’ operation > select the outer contour
line of the surface > select an interval distance of 3mm.

105
To split and close the existing curve:
3. Select the texturing Toolbar > select the ‘Split curve’ operation
4. Press Esc > Select and delete the smaller separated part of the curve
5. Select the ‘Close Curve’ operation > select the ‘Free curve’ option.

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Since this curve is connected with the surface, this will be first attracted on the surface, during this
operation this surface will also be split.
6. Select the Texturing toolbar > select the ‘Attract Curve’ operation > select the curve and the
surface.
The surface is created:
Task 3. Apply the 2D texture

The first step of creating a texture is selecting a bitmap which will be wrapped on the surface.
1. Select the Texturing Toolbar > select the 2D Texture operation. > select the surface to apply
the texture > select a bitmap, named ‘005_honeycomb’ > select ‘Apply’.

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To change the properties of the bitmap, select the 2D texture. You can select the 2D texture by clicking
on the 2D texture in the 3D view, or by opening the tree of the part in the Object Tree.
By changing the ‘Width’, you can rescale the part.

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Task 4. Convert to a 3D texture

Now the 2D texture is created, this can be converted to a 3D texture.
1. Select the Texturing toolbar > select the ‘2D to 3D Texture’ operation > select the parameters
below.
For all the black pixels we choose an offset of -0.4mm, for all the white pixels we choose an offset of 0.4
mm. Before selecting the ‘Apply’ button, estimate the Memory. This gives an idea if the operation will
succeed or not based on the capabilities of your system.

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/ Chapter 7: Export
Exercise 1: Anatomical Reverse Engineering
Medical imaging data, like CT or MRI, can be segmented to create accurate, patient-realistic, 3D models.
However, these complex, organic 3D models are generated in the STL file format, and this format is not
welcomed by traditional CAD softwares. Therefore 3-matic Research has an Anatomical Reverse
Engineering module. This module creates solid (C0-continuity) IGES files from your anatomical
models. And what is even better; it does so completely automatically.
1. Import the project ‘’FinishedFemur.mcs” into 3-matic Research.

2. Go to the Automatic Rectangular Patch option in the Surface toolbar and select Femur into
Entities selection box. The Part Complexity is measured automatically.

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3. Go to the File menu in the main toolbar. Select Export > Iges. Since the patching is already
done, the part only needs to be exported to Iges, so Patching can be checked OFF.

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Exercise 2: Export 3D PDF

The goal of this exercise is to export a 3D PDF along with measurements, analytical primitives, and
annotations created on the entity. The 3D PDF serves as an effective tool for communication of results
with the surgeon. It is possible to personalize the 3D PDF by including a header, footer, or both.
1. File > Open Project > DemoFiles > Mitral valve.mxp
2. Click on 3D PDF from the Export options under the File menu. The following operation page will
be opened.
3. In the Entities selection box choose all the objects that need to be shown in the exported 3D
PDF from the Object Tree. In this project we would like to show in the 3D PDF the distance
between the Mitral valve and the Papillary muscle of the heart to evaluate the optimal stent size.
The following objects need to be selected as Entities: Mitral valve surface, Mitral valve plane,
Heart, distance measurement and the annotations Mitral valve plane and Papillary muscle.
4. Choose the Output filename and directory by clicking on the path box.
5. In the Page Setup section select Both in the Header and Footer option.
6. Click on Image to choose an image or logo for the Header and Footer and change the
parameters according to the image.
7. Click on Apply.

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8. Open the resulting 3D PDF.
9. In the left panel of the 3D PDF the different views are listed. Click on Detailed View to see the
measurements, annotations and analytical primitives created on the exported entity.
10. When hovering the mouse pointer in the 3D area of the PDF, a toolbar will appear from where
different actions can be performed in the 3D PDF e.g. viewing more details in a cross sectional
view, adding comments, or making measurements in 3D PDF.

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Exercise 6. Creating Non-manifold Assembly for anatomical parts ...............................75

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/ Introduction to 3-matic Research

© 2018 Materialise N.V. All rights reserved.

Tutorial 3-matic Research 13.0 5/2018, L-10788 Revision 1

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1. Open a new 3-matic Research project.

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Exercise 2. Import a Mimics project file

Exercise 3. Import a CAD file of a heart valve

2. In the Import dialog, enable Fix normals and Stitch automatic.

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1. Go to Align and choose Arc to Arc Align.

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6. Apply and the result should look like this:

7. To open the inlet, delete or hide the surface.

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2. Try to Measure the wall thickness locally.

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Exercise 2. Curvature Analysis

2. Try to Measure the Analysis Locally.

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Exercise 3. Part Comparison Analysis

3. Set the Histogram range from -3 mm to 3 mm.

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4. Try to Measure the Analysis Locally.

6. Choose Entity as Aorta2 [Part Comparison Analysis].

7. Select Histogram range between -3.0000 and 3.0000.

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Exercise 4. Measure and analyze using fitted primitives

3. Click on Mark > Unmark All.

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7. Click on Mark > Unmark All.

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Exercise 2. Aneurysm design

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Exercise 3. Designing an acetabular cup

1. Import FinishedFemur.mcs (refer to Chapter 1: Import – Exercise 2)

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Exercise 4: Creating a Custom Cardiovascular Benchtop Model

Task Description Illustration 3-matic Research

3. Design base and Sketch

4. Add flange to the Import

5. Finishing touches Quick Label

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Task 1. Clean and Optimize the Geometry

Task 2. Add a Thickness and Trim the Model

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Task 3. Design Base and Supports