MimicsSECourseBook13 1

SE
Mimics Student Edition Course Book v13.1
Activating MimicsSE
Before you begin, you will need to activate MimicsSE. Each copy of MimicsSE should include a CCKey
that can be used to activate the software on one computer by following these steps:
1. In the Password Request Wizard, click License Server and then click Next. Copy the System
ID on the following page as it will be used later.
2. In the Password Request Wizard, Select Add a server.
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ii
3. Enter the appropriate information which will be provided by the person setting up the License
Server.
4. Click Next twice followed by Finish to finish activating the account.
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Table of Contents
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Activating MimicsSE ................................................................................................. i

Table of Contents .................................................................................................. iii
Introduction ............................................................................................................ 1
Materialise Overview .......................................................................................................... 1
Mimics history ..................................................................................................................... 1
From image to model .......................................................................................................... 1
STL file explanation ............................................................................................................ 2
Segmentation ..................................................................................................................... 2
Applications of Mimics ........................................................................................................ 3
RP ...................................................................................................................................... 3
CAE .................................................................................................................................... 4
Remeshing ......................................................................................................................... 5
Volume Mesh...................................................................................................................... 5
Material properties .............................................................................................................. 5
CAD.................................................................................................................................... 6
Surgical Simulation ............................................................................................................. 6
Discussion and Conclusion ................................................................................................. 7
Before You Start ................................................................................................................. 7
Install Libraries .................................................................................................................................. 7
How to Use this Tutorial.................................................................................................................... 7
Lesson 1: Mimics Navigation ................................................................................ 8

Image Views ....................................................................................................................... 8
Sagittal ............................................................................................................................... 8
Coronal ............................................................................................................................... 8
Axial ................................................................................................................................... 8
Mimics Interface ................................................................................................................. 9
Step by Step Tutorial .........................................................................................................11
Scenario: ......................................................................................................................................... 11
Navigation .........................................................................................................................11
Zooming and Panning..................................................................................................................... 11
Shortcuts ......................................................................................................................................... 11
Help Pages ..................................................................................................................................... 12
Project Management..........................................................................................................12
Project Management Toolbar ......................................................................................................... 12
Windowing ...................................................................................................................................... 13
Volume Rendering .......................................................................................................................... 14
Measurement Tools ...........................................................................................................15

Basic Measurements ...................................................................................................................... 15
Other Useful Tools .......................................................................................................................... 16
Homework 1 ......................................................................................................................16
Mimics Lesson 2: Basic Segmentation .............................................................. 17

Explanation........................................................................................................................17
Scenario: ......................................................................................................................................... 18
Thresholding Toolbar ...................................................................................................................... 18
Thresholding with Draw Profile Line ............................................................................................... 19
Region Grow ................................................................................................................................... 20
Calculate 3D ................................................................................................................................... 21
Crop Mask ...................................................................................................................................... 22
Edit Mask ........................................................................................................................................ 23
Dynamic Region Grow .................................................................................................................... 25
3D Tools.......................................................................................................................................... 26
Capture Movie ................................................................................................................................ 28
Homework 2 ......................................................................................................................28
Mimics Lesson 3: Advanced Segmentation ....................................................... 29
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Explanation........................................................................................................................29
Scenario: ......................................................................................................................................... 29
Multiple Slice Edit ........................................................................................................................... 29
Interpolate ....................................................................................................................................... 32
Edit Mask in 3D ............................................................................................................................... 34
Morphology Operations .................................................................................................................. 35
Boolean Operations ........................................................................................................................ 37
Measure Distances ......................................................................................................................... 37
Export to txt ..................................................................................................................................... 38
Homework 3 ......................................................................................................................39
Mimics Lesson 4: Surgical Simulation ............................................................... 40

Explanation........................................................................................................................40
Scenario: ......................................................................................................................................... 40
Cut .................................................................................................................................................. 40
Import and Reposition an STL ........................................................................................................ 43
Homework 4 ......................................................................................................................44
Mimics Lesson 5: CAD export ............................................................................. 45

Explanation........................................................................................................................45
Scenario: ......................................................................................................................................... 45
IGES Surfaces ................................................................................................................................ 45
Export to CAD ................................................................................................................................. 53
Homework 5 ......................................................................................................................53
Mimics Lesson 6: Centerline creation ................................................................ 54

Explanation........................................................................................................................54
Scenario: ......................................................................................................................................... 54
Calculate and Export Centerline ..................................................................................................... 54
Cut Centerline Ending..................................................................................................................... 57
Modify Centerline ............................................................................................................................ 58
Homework 6 ......................................................................................................................59
Mimics Lesson 7: FEA (part 1) ............................................................................ 60

Explanation........................................................................................................................60
Scenario: ......................................................................................................................................... 62
Remeshing ...................................................................................................................................... 62
Material Assignment ....................................................................................................................... 66
Export to FEA ................................................................................................................................. 70
Homework 7 ......................................................................................................................70
Mimics Lesson 8: FEA (part 2) ............................................................................ 71

Explanation........................................................................................................................71
Scenario: ......................................................................................................................................... 71
Non-Manifold Assembly .................................................................................................................. 71
Creating a Non-Manifold Assembly ................................................................................................ 71
Optimizing the Non-Manifold Assembly Mesh ................................................................................ 77
Splitting a Non-Manifold Assembly and Exporting the Remeshed Parts ....................................... 79
Creating a Volume Mesh for a Non-Manifold Assembly................................................................. 80
Homework 8 ......................................................................................................................81
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Mimics Final Project ............................................................................................. 82

Congratulations! ................................................................................................... 83
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Introduction
Mimics (Materialise's Interactive Medical Image Control System) is Materialises software for processing
medical images and creating 3D models. Mimics uses 2D cross-sectional medical images such as from
computed tomography (CT) and magnetic resonance imaging (MRI) to construct 3D models, which can
then be directly linked to rapid prototyping, CAD, surgical simulation and advanced engineering analysis.
Materialise Overview
Materialise is an international company, best known for its activities in the field of rapid, industrial, and
medical prototyping. Started in 1990 as a spin off corporation from the University of Leuven in Belgium, it
began as a rapid prototyping service bureau. Since then, Materialise has grown into the worlds largest
rapid prototype producer. The company also enjoys a worldwide reputation as provider of innovative
software solutions. As such, Materialise has acquired the position of market leader for 3D printing and
digital CAD software in addition to being a major player in medical and dental image processing and
surgery simulation.
For the medical and rapid prototyping industries, Materialise offers an array of software solutions; Mimics
is the medical image based processing tool for creating 3D models, and linking the models to rapid
prototyping (RP), computer aided engineering (CAE), computer aided design (CAD), and surgery planning.
SurgiCase CMF is Materialises CT based craniomaxillofacial surgical planning software. It allows users
to import patient data, create 3D models, plan out the surgery, and rapid prototype surgical guides that
can be used during the operation to match the surgical plan. SimPlant is Materialises dental implant
planning software. Similar to SurgiCase, it allows users to plan dental implant surgeries and prepare
surgical guides for the operating room. All medical software packages developed by Materialise are FDA
approved. Magics RP is considered a powerful preprocessor for additive fabrication. It prepares 3D
object (STL) files for additive fabrication as well as performs easy mesh and geometry manipulation. 3matic is Materialises forward engineering software that allows advanced manipulation and design on an
STL file. It allows a user to perform digital CAD operations (i.e. typical CAD operations on a STL file
instead of the traditional CAD files), and fix and remesh for CAE. Materialise ensures that all software
packages are ISO-9001 certified and that there is a seamless link between all packages.
Mimics history
After the start of the company Materialise in 1990 as a rapid prototyping company, it didnt take long for
the company to see the analogy between RP and CT (or MRI) images; in RP, a 3D model is built slice per
slice, whereas a CT scanner does the reverse, it breaks down a 3D model (the human body) into a stack
of image slices. In 1992 Materialise wrote software that linked the image information to RP models. The
software allowed extracting 3D information from an image stack and building a 3D model from it, using RP
technology. Materialises Interactive Medical Image Control System (MIMICS) was born.
From image to model

A stack of images can be loaded into the software, Mimics, and this usually consists of images in the XY
plane (axial images). Mimics then calculates and creates images in the XZ (coronal) and YZ (sagittal)
direction. This enables a more comprehensive 3D feel of the 2D data.
The key to converting anatomical data from images to 3D models is a process called segmentation.
During segmentation the user indicates the structure(s) of interest in the sliced image data. This
information is then used to recreate a 3D model from the segmented structures. To describe the outer
surface of the 3D model, Mimics uses the STL format, which is the common file format in RP. The STL
format allows describing the most complex geometries accurately. This is necessary, since anatomical
data is in general very intricate. Accurate segmentation is important in order to extract meaningful
information from images.
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STL file explanation

An STL file is a triangulated surface mesh file (Figure 1). The file contains the three nodes of each
triangle and defines the normal direction of the triangle. This file format is ideal for anatomical geometry
because of its simple file structure and flexibility to match any contour desired. It is not controlled by
parametric constraints such as true CAD files and IGES files.
Figure 1. Triangulation of an STL file.
Segmentation
The medical images coming from CT or MRI scanners consist of grayscale information. Mimics allows the
user to create models based on the gray values (Hounsfield units in CT images) within these images. A
gray value is a number associated with an image pixel defining the shade (white, gray, or black) of the
pixel. There is a direct association between material density of the scanned object and the gray value
assigned to each pixel in the image data. Because of this, Mimics has the flexibility to create models from
any geometry distinguishable within the scanned data. By grouping together similar gray values, the
image data can be segmented, and models created. This type of segmentation is called thresholding and
yields accurate models.
Many of the segmentation tools in Mimics are common in image processing and can be applied in any of
the views (XY, XZ or YZ). However, Mimics also has a unique 3D editing tool; an initial segmentation can
be optimized in a 3D preview (Figure 2). This makes editing very easy since it allows true editing in 3D,
which is easier to comprehend than 2D editing.
Figure 2. Editing a Mimics model in 3D to capture only the femoral head.
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Using the segmentation and known information on the pixel size and the distance between the image
slices, Mimics can calculate a 3D model (Figure 3). The accuracy in a Mimics model matches the
accuracy of an object captured within the scan.
Figure 3. 3D objects calculated from CT images.
Applications of Mimics
Although Mimics was originally designed to link medical images to rapid prototyping, there are of course
many applications possible using the 3D model that is calculated after segmentation. Over the years
Mimics evolved to the Golden Standard in linking medical images to various applications. Continuous
developments and the inclusion of new tools continue to widen the application base. The applications that
will be discussed here in more detail are:
Rapid Prototyping (RP)

Computer Aided Engineering (CAE)
Computer Aided Design (CAD)
Surgical Simulation
All these applications require slightly different processing before they can effectively be used. Mimics
development continuously strives to optimize this pre-processing to ensure a fluent workflow from
images to application.
RP
The 3D object created within Mimics is an STL file. STL is the common language for rapid prototyping
machines and 3D printers and it can describe very complex geometries (like medical geometries). The 3D
object can be directly exported to rapid prototyping in either STL or Sliced file format; in the latter it also
allows support generation. Or it can be imported into Materialises Magics program for support generation
or for build optimization. Figure 4 shows how models exported from Mimics were prepared in Magics to
generate supports and duplicate the object to print multiple models at once.
Figure 4. Mimics models printed on an RP machine with support generation.

Rapid prototypes from Mimics have many applications in the medical field. Considering the fact that the
human brain is optimized to work with something tangible, holding a physical model is always easier to
understand than a 3D model on a computer screen, no matter how realistic 3D graphics are.
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Since the models accurately match patient data, the models are helpful in communication and surgery
preparation for clinical work. Medical rapid prototypes are highly utilized by medical device design
manufactures and engineers. The RP models allow engineers to test form, fit, function, and validation of
designs on actual patient data prior to testing them on actual patients. Rapid prototyping also allows
users to test and validate designs with physical models.
CAE
Advancements in computer aided engineering (CAE) have provided engineers with the ability to test
designs prior to ever building a physical model. Analyses such as finite element analysis (FEA),
computational fluid dynamics (CFD), and kinematics allow researchers and engineers to put actual patient
data to the test without the inconvenience of physical testing. In FEA for example; a force is applied to a
certain anatomical part and CAE software then calculates the resulting stresses and strains. In order to do
so, CAE software divides the model into tiny, discrete elements and calculates the variables for every
element. The magnitude of the variable is usually visualized with color maps.
In the early days of CAE, people used CAD designs as a starting point for their geometrical input. For
analyzing bridges or buildings this is understandable, but complex anatomical data is impossible to design
in a CAD package. Starting from image information ensures accurate geometry, stored in STL format.
Since STL also uses small elements (triangles) to describe a 3D model, the link with this application is
obvious. For RP however, the shape of the triangles is not important, but for CAE it is; very sharp
elongated triangles are not suitable for analysis, since the stress in one end of the triangle can be
significantly different from the stress in the other end. Therefore for accurate analysis, CAE software
requires STL files that use equilateral triangles to describe the 3D. Figure 5 shows the difference between
an STL file prepared for RP compared to CAE. Hence, Mimics can optimize the shapes of the triangles
before exporting them for CAE analysis. Also to reduce the computation time in CAE software, the
number of triangles in a mesh must be reduced; this reduces the number of elements and nodes the
analysis programs have to calculate. The complete process of triangle shape optimization and triangle
reduction is called remeshing.
Figure 5. Differences between STL files of an abdominal aortic aneurysm prepared for rapid prototyping
(left) and FEA (right).
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Remeshing
Mimics has been designed to remesh 3D objects (STL files) from their original RP-ready format to a CAEready format. To optimize the mesh and create equilateral triangles, Mimics will analyze the shape quality
of each triangle. After the quality of each triangle within a mesh is understood, Mimics can automatically
perform the remeshing processes described in the above section. This will quickly prepare anatomical
models for CAE analyses. For highly sensitive analyses and for more user control and definition, Mimics
has the option to perform manual remeshing. This allows a user to manually edit triangles and control the
triangle reduction and size.
The remeshing process in Mimics also allows one to analyze an anatomical assembly. Researchers and
engineers alike will use Mimics to prepare a study of multiple anatomical models interacting together or
anatomical data interacting with manufactured device designs. While running a finite element analysis of
an assembly it is important for two mating surfaces to have node-to-node matching. Mimics will create
this node-to-node matching from two separate STL files as shown in Figure 6 and Figure 7.
Figure 6. Original mesh of two parts without node-to-node matching.
Figure 7. Two parts, with optimized mesh and node-to node matching.
By utilizing Mimics remeshing tools, a user can observe actual anatomical data reacting under applied
constraints (loads, flow, heat, etc.).
Volume Mesh
STL is a surface representation. To do an analysis, a complete volume description is needed. Generating
a volume mesh from an optimized surface mesh is straightforward. From a triangle surface mesh a
tetrahedral volume mesh can be generated. A tetrahedral and hexahedral mesh can be created within
rd
Mimics or within a 3 party volume mesh generation package. This volume mesh generation flexibility
allows a user to determine what parameters and settings are most important depending on application
and preference.
Material properties
Most CAE programs allow the user to assign constant material properties for individual objects.
Anatomical structures, such as bone, have varying material properties throughout the structure. In the
grayscale images from the CT scan there is more information than just the geometrical shape of an
anatomical part. As described in the section about segmentation, the gray values represent material
density. This information is used in Mimics to accurately assign material properties to the elements of the
volume mesh (Figure 8).
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Figure 8. Distributed material property assignment for an FEA analysis based on the gray values in a CT
scan. Color mapped visualization of the material properties of the different elements in a section of a
femur; the softer trabecular bone is blue/green, whereas the denser cortical bone is orange/red.
CAD
For engineers designing equipment such as medical implants and devices, Mimics has provided a link to
take patient data directly to the 3D CAD platform for design, verification, and sizing studies. The Mimics
CAD export allows users to create IGES curves and surfaces from anatomical surfaces and import them
into any CAD software.
For true CAD applications, the surface needs to be mathematically described (NURBS). This process of
reverse engineering is quite tedious and time-consuming and leads to a simplification of the surface. To
be able to design accurate implants, it is best to keep working on STL level. Also here, 3-matic (by
Materialise) fills a need; it allows design changes directly on the STL.
Surgical Simulation
Mimics helps bridge the gap between clinicians and engineers. With Mimics surgical simulation functions,
a surgery can be performed within the virtual world prior to entering an operating room (OR). Typical OR
procedures can also be performed in Mimics (e.g. cut, move, reposition, resize). Mimics can import
objects such as surgical guides, devices, and implants and position them as prepared for surgery.
A user can then begin to analyze the placement of the imported implant/device. This helps both
engineers designing the implant and surgeons placing the implant understand a designs fit and function
as in Figure 9.
Figure 9. Surgical simulation of the placement of a femoral implant.
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A user can use Mimics to study anatomy and create measurement studies to analyze and classify data.
With the ability to create unique measurement studies that can be applied to multiple datasets, the same
measurements can be acquired from various patients to aid research. Mimics can also calculate a
reconstructed X-ray from the image information. This is very convenient for clinicians who are used to
reading X-ray images. Figure 10 shows the anthropometric analysis tool and the ability to collect multiple
data points and measurements for further manipulation and understanding.
Figure 10. Anthropometric Analysis and the visualization of the analysis points on a reconstructed X-ray.
Discussion and Conclusion

Mimics is a powerful image processing tool and links to many applications. Its user base consists mostly
of engineers, but also clinicians. There are discrepancies in the demands of both engineers and clinicians
for software like Mimics. Engineers want a powerful open toolbox, whereas clinicians want it to be easy to
use and fast. To accommodate the wishes of both, Mimics is equipped with a very user friendly graphical
user interface (GUI) as well as powerful tools to analyze intricate data. Therefore, Mimics is an easy to
use, powerful toolbox for both engineers and clinicians.
As is clear from this chapter, Mimics provides a link to many applications. This opened up possibilities in
many markets. The major industries that use Mimics are Orthopaedic, Cardiovascular, and
craniomaxillofacial (CMF). Many tools within the software have been designed to fulfill needs and
requests of these markets. Other industries Mimics is also used in include tissue engineering,
anthropology, technical/industrial design, and pulmonary study. Because Mimics is used in multiple
markets, it is important for the software to have features that fit each market. Therefore Mimics has a
modular structure and users can tune the software to their needs by extending the basic package with
additional modules. Users of Mimics often identify tools that would make their research and work more
efficient. This user feedback is invaluable for the development of the software and to create a well
rounded, highly effective research tool.
Of course Mimics provides a seamless link with other Materialise software; Magics for RP applications
and 3-matic for CAE or design (CAD). E.g. 3-matic can design implants based on the image information
coming from Mimics and the design can then be verified again in Mimics on the image data of the patient.
Before You Start

Install Libraries
SE
Make sure to install the Anthropometry and Distractor libraries which can be found on the Mimics
CD.
How to Use this Tutorial

You will see the following conventions while following the step by step and homework sections of this
tutorial:
Anything in single quotation marks signifies exactly what you will see in Mimics.
Anything in italics and double quotation marks represents what you should type.
Phrases in bold represent tools in Mimics.
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Lesson 1: Mimics Navigation

Tools to learn: Navigation, project management, basic measurement tools.
Image Views
To process data in Mimics, a set of stacked 2D cross-sectional images is first imported. These 2D images,
commonly in DICOM format, come from medical scanning equipment such as CT or MR machines.
Mimics can also import micro-CT, bitmap, TIFF, and JPEG files. The quality of the 3D images that Mimics
can create directly correlates to the slice thickness and pixel size of the 2D images.
The imported images will appear in Mimics in three different views: axial, coronal, and sagittal. Engineers
can think of these as the top, front, and right views from their favorite CAD program.
Sagittal
Coronal
Axial
Usually, the stacked images will be obtained by the imaging equipment in the axial view. Mimics will then
calculate the remaining two views (in this case coronal and sagittal) by transposing the original images
into their respective positions.
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Mimics Interface
The main window is broken into four views: coronal, axial, sagittal, and 3D. The 3D pane is where 3D
models can be visualized. Clicking on an image with the left mouse button automatically updates your
location in all four views.
Each of the 2D views contains a slice number in the lower right corner. The view corresponding to the
original images (in most cases axial) also has a table position in the bottom left corner which describes
the slices location in reference to the origin of the scanner table.
The main toolbar contains dropdown menus for most of the tools available in Mimics. Below the main
toolbar is an icon list of frequently used tools.
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The project management toolbar is the database of all objects in Mimics. It contains tabs that correspond
to each of the different object types such as masks, measurements, 3D objects, and curves. In the tabs,
you will find the window where each object exists and all operations possible with that type of object. For
example, under the 3D objects tab you can create new 3D models and delete existing models, among
other things.
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Step by Step Tutorial

Scenario: As a radiologist, you need to navigate through a patients scanned images and take certain
measurements to aid in your diagnosis. The procedures outlined below will show you how to accomplish
these tasks.
Navigation
Zooming and Panning
Start by opening the skull_se.mcs project.
Zoom allows you to view a close-up of a selected region. Panning moves an image up, down, left or right.
1. Click on the Zoom tool
in the main
toolbar.
2. Drag a box around the axial view of the
image by holding down the left mouse
button.
3. Select the Unzoom tool
and click on the same image you just zoomed in on.
4. To create a full screen view, select Zoom to Full Screen

and click anywhere on the images. To
restore the images size click on Zoom to Full Screen again.
5. Select Pan Once
in the main toolbar. Left click and drag on a view to pan an image.
6. Click on Unzoom and then the view you want to restore to return the image to its original location.
Shortcuts
Key combinations can be used in place of certain tools, like the tools learned in the Zooming and Panning
exercise. These shortcuts can help optimize image processing and workflow.
Try out some navigation shortcuts by using the following commands:
Right mouse button Rotate 3D objects: Move the mouse while holding the
right mouse button down. This only works when the
mouse is in the 3D pane.
Change contrast of 2D views: Move the mouse while
holding the right mouse button down. This only works in
the axial, sagittal, and coronal views.
SHIFT + Right mouse button Pan: Move the mouse while keeping the buttons pressed.
CTRL + Right mouse button Zoom: Move the mouse vertically while keeping the
buttons pressed to zoom in and out.
Arrow Up/ Page Up Rotate up with discrete steps.
Arrow Down / Page Down Rotate down with discrete steps.
Arrow Right / End Rotate right with discrete steps.
Arrow Left / Home Rotate left with discrete steps.
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Help Pages
The help pages contain in-depth information about tools and tabs.
1. Click on Help in the main toolbar then
General Help to access the help files.
2. Click the red X to close the help files.
3. Click on the Context Help icon
in the main toolbar and then click on any tool to view its help file.
Note The step of importing images is not explained in this tutorial since Mimics Student Edition does not
allow importing. However, information on importing images can be found in the help files under the Contents
tab by selecting Mimics Tutorial and then Import.
Project Management
Project Management Toolbar
The project management toolbar consists of tabs which give an overview of all of the objects in a
project.
1. Select the Project
Management button
to
make this toolbar visible if it is
not already.
Each tab of the project management toolbar represents a type of object in Mimics. All of the objects
for a project are shown here. The most frequently used tools for each tab are located along the
bottom of the tab; however, the full list of tools can be seen by clicking on the Actions button
2. Click through the tools of the different tabs to familiarize yourself with what is available.
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Windowing
The gray values of CT images are expressed according to the Hounsfield scale shown below, which
has 4096 values. To map this scale onto the 256 gray values of your computer, Mimics has a feature
called windowing. Windowing is a tool to adjust the image contrast.
1. Change the contrast of the

images by moving the line or
the endpoints on the graph
located in the Contrast tab of
project management.
The histogram pictured shows the window of pixels mapped in the image. The shortcut for changing
the contrast of an image is to right click on an image and drag the mouse.
2. Select different contrasts in
the drop down menu.
Notice how different scales
allow better visualization of
certain tissues.
Differences between fat, soft tissue, muscle, and even bone can be emphasized depending on the
window chosen.
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Volume Rendering
Volume rendering allows you to quickly visualize your 2D data as a 3D object without having to take
the time to segment and create a model. It is only a visualization tool, but gives a nice impression of
what your model will look like.
1. Go to the Volume Rendering tab at the bottom of the project management tabs and select
Bone and Soft Tissue from the pull-down menu.
2. Turn on volume rendering
by clicking the Volume
Rendering button
the 3D toolbar.
in
3. Go through the pull-down menu selecting the different predefined settings to see all of the
visualization options.
4. Turn off volume rendering by clicking the Volume Rendering button
again.
Volume rendering can consume a lot of system resources slowing down computer processing time, so
remember to turn it off when you are done.
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Measurement Tools
Basic Measurements
Different tools are available to collect information from scanned images. Measure Distance and
Measure Angle calculate data from either the 2D scans or 3D model. Any of these measurements
can then be exported to text for further analysis in statistical packages.
1. Scroll to axial slice 180.5 and click Measure Distance
toolbar.
under Measurements in the main
2. Click once on one side of

the skull and again on the
other side, creating a
horizontal line.
The measurement is displayed on the screen and in the Measurements tab of the project
management toolbar. To hide the measurement simply click on the eyeglasses in the tab.
3. Scroll to axial slice 69.5. In the Measurements tab of the project management toolbar, click
on the New button
and then select Measure Angle
4. Measure an approximate
angle of the jaw by clicking
once to start the
measurement, click again to
select where the angles
vertex is, and click once more
to end the measurement.
To change the location of the endpoints or vertex of the angle, drag the crosshairs.
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Other Useful Tools

Measure Density measures the area, mean value of the density, and the standard deviation of a
selected region. Annotations can be used to point out measurements or structures in the images.
1. Scroll to axial slice 113.5.
2. Select Measure Density in
Ellipse
from the
Measurements menu and
select the circular area of the
sinus cavity. Notice that this
tool gives you the area of the
ellipse, mean Hounsfield unit,
and standard deviation from
the mean.
You can change the size of the density tool by grabbing the handles. As you scroll through the image,
the location of the measurement will not change. The same type of tool is also available in a
rectangular shape: Measure Density in Rectangle
3. Select the Annotations tab and click New
.
.
4. Next click the image near the

elliptical measurement; this is
where the annotation will be
placed. Type sinus cavity in
the Text: section and click
OK.
The annotations text can be moved by left clicking on the text and dragging.
5. Save the file as Lesson1_your name.
Homework 1
Using the dataset from Lesson 1, find the following measurements:
1. Vertical distance from the base to the top of the skull.
2. Angle between the spine and the bottom the mandible. Hint: Use the Atlas (C1 vertebra) as the vertex
for this angle
3. Density of the superior region (top) of the skull.
For each of the measurements taken, state which of the three views were used.
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Mimics Lesson 2: Basic Segmentation

Tools to learn: Thresholding, region growing, dynamic region growing, calculate 3D, basic
editing tools, create movie.
Explanation
The first step in creating a 3D image from 2D data is segmentation. Mimics has several tools to segment,
or section, regions of interest. For example, Thresholding is used to classify all pixels within a certain
Hounsfield range as the same color, or mask. By setting only a lower threshold value, all pixels higher or
equal to the set value will comprise the same mask. Alternatively, an upper and lower threshold value
can be set. In this case, the pixels falling within the designated range will make up a single mask.
Drawing a Profile Line can be helpful with setting threshold values since it shows how the gray value
changes along a line in an image. Different sections of an image can be highlighted using different masks.
The mask that is selected in the project management Masks tab is considered the active mask.
After thresholding, a mask may need to be separated into numerous objects. Region Growing allows
just this and is also useful for removing floating pixels. With Dynamic Region Growing thresholding
does not need to be done first. Instead, Mimics creates a mask based off of how surrounding pixels
compare to a selected data points gray value, automatically determining threshold values. This tool
proves very useful for segmenting structures such as blood vessels and nerves.
To further segment various parts of an image, Mimics has a selection of editing tools. Edit Mask provides
the tools needed to draw, erase, or locally threshold a specific mask. Crop Mask restricts segmentation
to a designated area by removing everything from a mask that is outside a selected bounding box.
To perform the transformation from 2D into 3D, Calculate 3D is used. Different options are available for
the quality of 3D model created. Low and medium quality have short calculation times but may produce a
more approximated model. High quality can give a smoother, more accurate model, however the most
accurate will be from using the optimal setting. If necessary, 3D calculation parameters can be set
manually using the custom setting. For more information on quality settings and parameters, see
Calculate 3D in the help files.
Depending on the type of file output needed, Mimics has various exporting options including exporting in
the STL format or even exporting movies.
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Scenario: Your boss has asked you to review some scans and put together a presentation displaying a
patients anatomy. You will use Mimics to highlight the bone structure of the hip, show where the aorta
lies in relation to the hip, and create a 3D model to fully display the patients anatomy. The procedures
outlined below will show you how to accomplish these tasks.
In this section, you will use two different methods to create a mask displaying the hip. Then you will
calculate 3D models of both masks.
Thresholding Toolbar
Thresholding classifies all pixels within a certain Hounsfield range as the same color, or mask. There
are predefined settings for certain biological materials available in the thresholding toolbar. A lower
threshold allows segmentation of soft tissue, whereas a higher threshold segments bone.
1. Open the hip_se.mcs project.
2. Select Thresholding in the main toolbar under segmentation.
3. Click through the predefined

thresholds to view how different
thresholds highlight different areas
of the images.
You can manually set the threshold by changing the minimum and maximum values.
4. Select the Bone (CT) threshold
and click Apply.
A mask is visible when the eyeglasses under the Visible column of the Masks tab are showing. A
mask is considered active when it is highlighted. Any editing will be performed on the active mask.
5. Rename the mask BoneThreshold by clicking Green in
the Masks tab until you see a
blinking cursor signifying the text
can be changed.
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Thresholding with Draw Profile Line

Draw Profile Line is another way to threshold an image, as done in the previous exercise. This tool
displays how the gray value changes along a line within the image.
1. Scroll to axial slice 40. Select New
Mask
2. Select Draw Profile Line

under
Measurements in the main toolbar.
The cursor will turn into a pencil.
3. Click once below the femur to start the

profile line and once above the femur
to end the profile line.
You want the profile line to cross over your region of interest and into surrounding regions. You will see a
spike at the beginning and end of the graph as the profile line transitions from soft tissue to bone and then
back to soft tissue. Clicking Scale to Fit provides a zoomed in view of the peaks along the profile line.
4. Leave the upper threshold at 1634 and the lower threshold at 226.
You can move the upper and lower threshold values by clicking Start thresholding in the Profile Lines
dialog box. You will see horizontal lines to indicate these values. Lowering the threshold selects soft
tissue and increasing the threshold selects dense cortical bone. Threshold values can also be changed
in the Thresholding dialog box. In this case a good threshold for bone is the predefined bone (CT) setting
which is 226 to 1634. Otherwise, a rule of thumb for selecting bone on CT images is to put the lower
threshold on 1/3 of the cortical peak.
5. Click Start thresholding in the

Profile Lines dialog box.
6. Hit Apply in the thresholding
dialog box since we are
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keeping the 226 and 1634
threshold values. Click Close
in the Profile Lines box.
7. Name the mask Bone-Profile
line.
You will see the profile line appear in the measurement tab of the project management toolbar. If you
need to find where a profile line is located, click the Locate button
Region Grow
Region growing is used to separate masks into different parts as well as to get rid of floating pixels.
Remember that thresholding must be done prior to region growing.
1. Select Region Growing
from the Segmentation toolbar. The mouse will turn cross-shaped.
2. Select Source (= BoneThreshold) and Target mask

(= New Mask). Keep Multiple
Layer checked so region
growing will be done on the
entire dataset instead of just
one layer.
3. Make sure Leave Original
Mask is checked.
If you uncheck Leave Original Mask, all selected information will be removed from the target mask and
placed in the source mask (compare it to cut and paste).
4. Click somewhere on the hip.
Rename this new mask
Bone2-Threshold. Select
Close to get rid of the region
growing toolbar.
You will notice that now the cyan mask only contains bone, unlike the green mask which included other
structures as well.
5. Repeat the procedure
for region growing on
the Bone-Profile line
mask. Name the new
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mask Bone2- Profile
line.
This step is needed so that later we can compare the 3D models of the mask created using thresholding
versus the mask created using draw profile line.
Calculate 3D
Transform data from the 2D images into a 3D model.
1. Click on the Bone2threshold mask in
the Masks tab of
the project
management
toolbar.
2. Select the Calculate
3D button
This button can be found at the bottom of the mask tab, under segmentation in the main toolbar, or in the
icon list on the main toolbar. Most major tools have three locations; in their corresponding tab of project
management, under their specific heading in the main toolbar, and as an icon in the main toolbar.
3. Make sure the Bone2-Threshold
mask is highlighted and select high
quality. Click Calculate.
Custom parameters can be set for the 3D calculation. For more information on these settings look under
calculate 3D in the help files. If a message pops up saying the resulting 3D model will consist out of
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different parts, click No. Receiving such a message indicates that your mask contains multiple
disconnected objects; unless you want this, you should perform a region grow on the mask.
4. Rotate the 3D model by holding the left mouse button in the 3D view and moving the mouse
around.
Clicking near the center of the object will rotate around the vertical and horizontal axes. Clicking outside
the center of the object will rotate around the axis perpendicular to the viewing angle. If you want to
remove the toggle reference planes from the 3D pane, click Toggle Reference Planes
5. Calculate a 3D model
of the Bone2- Profile
line mask using the
same procedure as for
the Bone2-Threshold
mask. You will notice
that both masks result
in the same 3D model
even though different
thresholding methods
were used to create
them.
Editing Tools Now we will crop the image to show only the region of interest and perform editing to
separate the pelvic bone from the vertebral column.
Crop Mask
With Crop Mask you can manually change the boundaries of your mask or enter the desired
coordinates.
1. Select the Bone2- Threshold mask.
2. Click on Crop Mask
under Segmentation.
3. Enter the following

coordinates so that only
the lower portion of the hip
and spine are shown in the
mask.
You can also crop the mask by resizing the bounding box on the image.
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4. Click OK.
Now the mask will only be shown in the region that was outlined by the crop mask bounding box. (To
achieve the same view as the pictures for step 4, the other masks visibility have been turned off)
Edit Mask
The area contained within a mask can be modified using the edit mask tools. We will use such tools to
separate the vertebral column from the pelvic bone.
1. Make sure the Bone2Threshold mask is
active. Zoom in on axial
slice 115.
2. Click Edit Masks
under Segmentation and select Erase in the Edit Masks toolbar.
3. Set the Type: to circle, check the Same Width & Height box, and set the Width: to 20 (the height
will automatically be changed to 20 also).
4. Erase the area where the
vertebral column and pelvic
bone meet by holding down
the mouse and dragging the
cursor over the area to be
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erased. The erased region
will turn from the original
color of the mask to the
original scan data.
Other tools in Edit Masks include Draw which adds pixels to the active mask and Threshold which applies
a local threshold of your choice to the area you select.
5. Scroll up through slice 175
continuing to erase the pelvic
bone on each slice.
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6. Do a region grow on the
vertebral column and calculate
a 3D model on high quality.
Since we separated the pelvic bone, only the vertebral column should appear in the 3D model. If your
model has more than this, there is most likely a connection that has not been broken. You will need to go
back through the slices to do editing to break this connection.
Dynamic Region Grow

Dynamic Region Grow allows you to grow a mask from a selected point without having to threshold
first. It is extremely useful for vessels, nerves, and arteries.
1. Make sure the Bone2- Profile line
mask is highlighted in the Mask tab
then scroll to slice 70 in the axial view.
2. Click on the Dynamic Region
Growing tool
. Check the
Multiple Layers and Fill Cavities
boxes.
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3. Click on the aorta and then rename
the mask Aorta.
4. Calculate a 3D model of this mask on

high quality. Some vessels branching
off of the aorta will be visible.
3D Tools
The 3D tools allow different visualization options for the 3D model as well as provide information about
the model.
1. Click Properties
3D objects project
management tab.
in the
Here you can change the color and name of the 3D model. If you click Details>> you will notice several
measurements including surface area and volume.
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2. Click on the
Aortas glasses
under Visible in
the 3D Objects
tab. This hides
and unhides the
3D model.
3. In the same tab,

click on the eye
glasses in the
Contour Visible
column and the
Visible column for
Bone-threshold.
When a 3D model is visible, clicking the contour visible eyeglasses will highlight the contours of the 3D
object in the 2D views.
4. Now click the eye glasses under the
Triangle Visible column.
This option allows you to view the triangulated surface mesh of the object. For better visualization of the
triangles, zoom in on the 3D image (hold Ctrl and the right mouse button while moving the mouse
vertically).
5. Click the same eye glasses to turn the triangle visibility off.
6. Select Toggle Transparency
in the 3D toolbar. You are able to view the internal shape of
the 3D object. Click Toggle Transparency again to return to normal.
7. Select Enable/disable clipping
also in the 3D toolbar.
Clipping slices the 3D model according to the view you select, displaying the objects cross-section.
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8. In the
Clipping tab
make sure
the box under
Active is
checked next
to Axial.
9. Scroll through the axial view to move the clipping plane.

10. To clip according to another viewing plane, simply select that view under Active (example
sagittal or coronal). You can also change the texturing of the cross-section by clicking on
Texture and changing it from object to slice to none.
11. Save the file as Lesson2_your name.
Capture Movie
Movies can be tailored to highlight different features depending on the application.
1. Click Capture Movie under Export in the main toolbar.
Under View to capture you can select which portion of the application you want to be included in the
movie. Options range from the whole screen to just selected views. Note the output directory. You
can change this to output to whatever file you want.
2. Select Bottom Right View for View to capture so that only the view containing the 3D model
will be included in the movie.
3. Hit the Record button
to start the movie. Rotate the image around, zoom in and out, and
pan the image as you choose.
4. Click Stop
when you are finished creating your movie. The movie will automatically open
in the software you have set up on your computer to view digital media.
Homework 2
On the skull_se.mcs dataset, perform the appropriate thresholding and region growing to segment and
then calculate 3D models of the following:
1. Soft tissue Hint: You may need to specify custom threshold values so that the scanner equipment
supporting the patients head is not included in this mask.
2. Mandible
3. All bone, including the mandible.
(Optional) 4. Export a short movie showing the models youve created.
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Mimics Lesson 3: Advanced Segmentation

Tools to learn: Morphology operations, Boolean operations, multiple slice edit, edit mask in 3D,
measurement tools.
Explanation
Segmentation will always follow a procedure of threshold to select a region of interest, region grow to
remove floating pixels, and edit mask to focus on an area of interest. The previous tutorial on
segmentation gave you the basic tools needed to manipulate scanner data. However, Mimics contains
various advanced segmentation tools such as Multiple Slice Edit, Morphology Operations, and
Boolean Operations that allow quicker and easier segmentation.
Multiple Slice Edit can be used to copy the editing done on a single slice onto other slices. This is useful
especially for eliminating scatter or disconnecting two body parts that touch in more than one slice. When
two elements need to be disconnected yet have a point of contact that is difficult to identify, Morphology
Operations becomes useful. Another handy tool is Boolean Operations which allows the visualization
of different combinations of two masks including the subtraction of one mask from another as well as the
intersection and union of two masks. Editing can even be done in the 3D view with Edit Mask in 3D.
With this tool you can immediately see how the editing you do changes the 3D model.

Scenario: As a researcher you want to explore the interaction between the heart and the aorta;
however, before further analysis can occur the aortas connection with the spine must be broken. You
can use the tools in Mimics to break this connection and also find out more information relevant to your
research. The procedures outlined below will show you how to accomplish these tasks. Assume this
patient has some type of stent supporting his or her aorta.
Advanced Segmentation First, separate the spine from the aorta using segmentation tools.
Multiple Slice Edit

Multiple Slice Edit is a timesaving tool because it allows you to apply the manual editing done on one
slice to other slices.
1. Open the heart_se.mcs project.
2. Create a threshold using the predefined Bone (CT) setting.
A bone threshold works well for this dataset because a contrast agent has been added so that the blood,
or lumen, appears brighter and images similar to bone. This provides for better visualization in the CT.
3. Do a region grow to get
rid of floating pixels by
clicking on the mask in
some part of the spine.
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4. Select the yellow mask and click Duplicate Mask
Rename the cyan mask Spine.
in the project management Mask tab.
5. Under Segmentation in the main toolbar click Multiple Slice Edit
6. Change Copy to slices: to Sagittal and make sure Select is marked.
Select adds pixels to a slice and deselect removes pixels. You can control the size and shape of your
editing tool by changing type, width, or height. For this exercise a circle of width and height 20 works
well. Changing the amount of slices the mask is copied to is possible by increasing the amount of slices
in the pull-down menu near Copy to slices. We recommend keeping this number low so you can
evaluate each selection as you scroll through the slices.
7. Shortcuts for multiple slice edit:
CTRL + left mouse button
Changes size of cursor
s key
Switches to select mode
d key
Switches to deselect mode
8. Scroll to slice 114.26 in the

sagittal view and highlight
the region of the spine that
borders the aorta (as
shown in the picture). Set
the Copy to slices to 1.
Press the green up arrow,
the mask is now copied to
the next slice.
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9. Repeat the above step
through all the sagittal
slices up through slice
134.77. Make sure to
modify the mask, changing
it as needed as the
boundary of the aorta and
spine moves. The pictures
show examples of slice
126.46, 129.39, and
130.37. Click Apply when
done.
Be careful not to include the aorta in your highlighting. If some of the aorta is selected by accident, use
Deselect to erase. If you need to select more of the spine, use Select.
10. Click the region grow tool
and then click on the aorta
(shown in pink).
The aorta should now show up in a mask of its own, separate from the spine. If it does not, this means
the aorta is still connected to the spine somewhere and you need to scroll back through the images to
delete this connection.
11. Rename this mask Aorta then
calculate a 3D model on high
quality.
Depending on how well you separated the aorta from the spine, your 3D model might contain some small
vessels branching off of the aorta. Later in the tutorial you will learn how to edit these using Edit Mask in
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3D.
You can choose different quality settings for 3D
model calculation. Low and medium quality create
faster models that have smaller file sizes; however,
the accuracy of the model is more approximated.
High and optimal quality models have better
accuracy but take longer to compute and are larger
files. For more information about 3D settings see
the help files.
Alternatively, the 3D LiveWire

tool can be useful for segmenting certain anatomy such as in lowcontrast images or MR. You select contours for a region of interest and 3D LiveWire creates a mask of
the area. Check out the help file titled 3D LiveWire for more information on this segmentation tool.
Interpolate
Interpolate creates a temporary mask that extends between two selected slices. This takes the place of
doing manual editing on many slices.
1. Click the glasses under Visible to hide the 3D model created above.
2. Create another duplicate of the yellow mask by selecting it and clicking Duplicate
the new mask Aorta-interpolate.
. Rename
We will accomplish the same task of separating the spine from the aorta using an alternate method.
3. Under Segmentation in the main toolbar click Multiple Slice Edit
4. Change Copy to slices: to Sagittal and make sure Select is marked.

5. Highlight the spine
on sagittal slice
113.28 to break
connections
between the spine
and aorta.
6. Scroll to slice
125.98 and
highlight the spine
again.
7. Click the interpolate tool
then click Apply.
The interpolation algorithm requires a selection in at least two slices with at least one empty slice in
between.
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8.
Repeat the interpolate

procedure with the first slice
as 126.46 and the last slice
as 132.32.

aorta, rename the mask
Aorta2 and then calculate a
high quality 3D model.
The aorta is now separated from the spine with a few quick steps. Again, you may see some branching
off of the aorta depending on your previous editing.
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Edit Mask in 3D
Editing can be done on a mask in the 3D view; however a new 3D model must be calculated after editing
is done in order to view the changes.
1. Click the New button
in
the project management Mask
tab.
2. Set the lower threshold
value to 270 then click
Apply.
3. Click the Region Grow
tool and select the
heart. Name the
resulting mask Heart.
4. Calculate a 3D model
on high quality.
In the 3D model you can see the vasculature branching off of the heart.
5. Select Edit Mask in 3D under Segmentation of the main toolbar.
You will use this tool to remove some of the small vessels coming off of the heart.
6. Increase the bounding
box in the 2D views to
include more of the
vessels.
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7. Make sure Select is
picked in the Edit Mask
in 3D dialog box.
Highlight the majority of
small vessels branching
off of the heart.
Rotate the model to access all of the vessels. Once an area is selected it turns a different color.
8. Click Remove and the vessels disappear from the 3D view.
9. In one of the 2D views, do a region grow on the Heart mask you modified in the previous steps.
10. Calculate a 3D model of
the new mask on
medium quality and
notice how the vessels
you deleted are gone.
11. Save the project as Heart_your name.
Morphology Operations
Morphology operations take or add pixels to the source mask. You can use a morphology operation as
an alternative to multiple slice edit for separating the aorta from the spine.
1. Create a duplicate of the Aorta mask. Name the mask Morphology_Aorta.
2. Click Morphology Operations
under Segmentation in the main toolbar.
3. Select Erode with Source: Morphology_Aorta, Target: <New Mask>, Number of pixels: 1, and
8-connectivity. Click Apply.
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Erode takes away the number of pixels selected and dilate adds the number of pixels to the boundary of
the mask. Open performs an erode followed by a dilate. This is useful for breaking small connections.
Close performs a dilate followed by an open; useful for filling cavities within a mask. 8-connectivity
considers only pixels in the surrounding plane whereas 26-connectivity looks at neighboring pixels in 3D.

aorta and name the
resulting mask
Erode_Aorta.
5. Change the color of the
Erode_Aorta mask to light
blue so you can see the
effect of performing an
erode.
6. Select Dilate with Source: Erode_Aorta, Target: <New Mask>, Number of pixels: 1, and 8connectivity. Click Apply and name the resulting mask Morphology2_Aorta.
7. The erode broke any connections between the aorta and spine. This allowed just the aorta to be
selected after a region grow. However, now the mask is one pixel smaller so dilate must be used
to return the aorta to its original size.
8. Calculate a 3D model on high
quality.
9. If you notice spikes on the aorta resulting from the patients stent, use Edit Mask in 3D to get rid
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of the protrusions and then recalculate the 3D model.
Boolean Operations
Boolean operations allow different combinations of two masks. We will use this tool to simulate the
wall thickness of the aorta.
1. Perform a Dilate of 3 pixels on the Morphology2_Aorta mask. Name the new mask Bool.
2. Select Boolean
Operations
from
Segmentation in the
main toolbar. Make
sure Mask A: Bool,
Operation: Minus,
Mask B:
Morphology2_Aorta and
Result: <New Mask>
are all selected.
In this case the Morphology mask will be subtracted from the Bool mask to simulate the wall thickness
of the aorta. Keep in mind that this is not the true thickness of the aorta but merely a visualization aid.
Other Boolean operations include finding the intersection and the union of two masks.
3. Click Apply.
4. Calculate a 3D model on
high quality.
Measure Distances
Distances can be taken from one point to another point on a 2D image or along a 3D surface.
1.
Select the 3D model previously created in the Boolean operations exercise.
2.
In the Measurements tab of project management click the New button

Distance Over Surface.
and then Measure
This measurement tool measures the shortest path along a surface between two points.
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3. Click on the top of the aorta and then
the bottom to get a distance along its
surface. Double click to finish taking
the measurement.
4. Now click Measure Distance
under Measurements in the main toolbar.
5. Zoom in on axial slice 106.88. Click

once on the image on one side of the
aorta and again on the other side.
6. This gives us a quick diameter for the aorta.

7. Save the project as Lesson3_your name.
Export to txt
Any measurements taken can be exported for further analysis.
1. Go to Export in the main toolbar and select Txt.

2. Select the measurements
you want to export and click
Add.
3. Select an output directory by

clicking the folder icon
4. Click OK to export the measurements to whichever output directory you have selected.
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Homework 3
Re-open the heart_se.mcs dataset.
1. Perform the steps needed to threshold so that you have a mask for only the lungs. Create a 3D
model. Hint: Think about what is inside of the lungs and how you would threshold to capture this.
2. Create separate masks for the aorta and spine using Boolean operations. In the lesson, sections
of the spine were removed to segment the aorta. This time, try editing the aorta to segment the
spine first.
3. Segment the heart. You may wish to perform some edits to remove the inferior vena cava, to
obtain a cleaner model.
Your final result should be four separate 3D models showing the lungs, spine, aorta, and heart.
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Mimics Lesson 4: Surgical Simulation

Tools to learn: Cut, split, position an implant, import an STL.
Explanation
Mimics Simulation module allows the simulation and planning of surgeries. Professionals in the
orthopedic and maxillofacial fields often prepare for their surgeries using this module. Just like in surgery,
you can make cuts, split and reposition parts. If a portion of a patients anatomy is missing, the mirror tool
can be used to reflect the anatomy across a plane. After cutting and repositioning, soft tissue simulation
demonstrates how the soft tissue will change with the modifications made.
Simulation also gives you the flexibility to test out different implant sizes and designs with a patients
anatomy. This helps a surgeon validate their implant selection. As an engineer, the simulation module
aids in the design process. The models created in Mimics can provide an engineer with a better
understanding of the geometrical constraints in biomedical design. After the anatomy is modeled, an
implant design can be imported into the Mimics platform to test form, fit and function. With the use of
Mimics a design can be validated both geometrically, in measurement studies for example, and
analytically, like with advanced engineering analyses.

Scenario: You are a maxillofacial surgeon presented with a patient who has a diseased portion of the
jaw and requires an implant. Use Mimics to prepare for your surgery by determining the cuts you will
make to remove the diseased portion of the jaw and where you will position the needed implant. The
procedures outlined below will show you how to accomplish these tasks.
Surgical Simulation
Cut
Cutting can be done in either 2D or 3D. You have the ability to change the orientation and size of the
cutting plane.
1. Open the skull_se.mcs project.

2. Click on Thresholding and select the
predefined Bone (CT) setting.
3. Select Region Grow and then click on the

mandible in the sagittal view. Name the
mask Mandible.
4. Create a 3D model using high quality.

5. Click on Cut with Polyplane
under Simulation in the main toolbar.
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6. To make a cut, click once

behind the last molar and
double click your second point
at the base of the mandible.
You can change the orientation of the cutting plane by dragging the red arrowhead. If you cannot see the
red arrowhead, left click on the plane and the arrow will reappear. The plane itself can be moved by
dragging the green points located on each end of the cutting plane. Adjust the points as needed to make
the cut as vertical as possible.
7. Select Properties in the
Cut with Polyplane
dialog box. Rotate the
model and change the
depth as well as any
other dimensions
needed to make the cut
go all the way through
the jaw (these
dimensions will vary
depending on where you
place your plane).
In the cutting plane properties dialog box you can change the depth, thickness, and extensions at the
front and end of the cutting path. There is also a preview option to visualize how the plane will look with
the specified dimensions.
8. Click Preview to view where the plane will cut and if everything looks okay, click OK to apply. If
the plane is not cutting where you want, readjust its dimensions.
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9.
Make sure the jaw is

selected under Objects
to Cut and your cutting
path is selected, then
click OK.
The cut will show up in the 3D objects tab as PolyplaneCut-Mandible.

10. Click on Cut with Polyplane
under Simulation in the
main toolbar to make another
cut.
11. Make sure PolyplaneCutMandible is selected under
Objects to cut: and CP2 is
selected under Cutting paths:.
12. Place your cutting plane
behind your first cut. Click
OK when you are happy with
the placement of the cutting
plane.
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13. Choose Split
under
Simulation to split the parts
along the cuts. Make sure
PolyplaneCut-Polyplane CutMandible and Two largest
parts is selected.
14. Click OK and notice the
middle portion of the jaw is
removed. This simulates
removing a diseased portion of
the jaw.
Import and Reposition an STL

The jaw implant we will use is an STL file. After importing STL files, you can use the repositioning tools to
place parts in the correct anatomical location.
1. To view the jaw implant, click on the eyeglasses next to jaw_implant in the STLs project
management tab.
If you cannot see the jaw implant in your 3D screen, you may need to zoom out to see where it is located.
Since the student edition of Mimics does not allow STL import, the jaw implant is already available to you
in the STL tab. However to load an STL in the professional version of Mimics, you would click on Load
STL
in the STLs tab, select the STL of choice, and then click Open.
2. Select Reposition
under Simulation in the
main toolbar. Make sure
the jaw implant is
selected under Objects
to Reposition and click
Move with Mouse.
To move the implant in either the x, y, or z direction pull on the corresponding axis. To move the implant
to a particular spot (not along an axis), you can grab the yellow rectangle at the origin of the axes. The
distance you want to move in a specific direction can also be entered manually into the coordinate boxes.
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3. Click Rotate with
Mouse. Grab each
of the different
rotation handles to
become familiar
with which ring
causes rotation in
which direction.
To change the rotation center, grab and move the yellow rectangle in the middle of the tool. The Move
and Rotate
tools can also be found in the 3D Objects tab.
4. Use the tools in

Reposition to place
the implant on the
mandible as shown.
5. You can save the location of a 3D object by clicking Save Position in the Reposition the 3D
Objects dialog box. Once a position has been saved, you can move a 3D object to that position
by clicking Go to saved pos. Selecting Go to home pos will move the 3D object to its original
location.
6. Save the project as Lesson4_your name.
Homework 4
Simulate the insertion of an orthopaedic implant using the femur_se.mcs project.
1. Make a cut through the femoral neck to remove the femoral head.
2. Insert the STL part, femur_implant, into the femur as shown.
3. Click the Contour Visible eyeglasses in the STL tab to show the
position of the implant on the CT images. Verify that the implant is
correctly positioned within the femur by scrolling through the images.
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Mimics Lesson 5: CAD export

Tools to learn: Polylines, IGES surfaces and curves, export to CAD.
Explanation
The MedCAD module acts as a bridge between medical imaging and traditional CAD design, such as
SolidWorks, Pro/Engineer, and Catia. An important feature of MedCAD is the ability to work with polylines.
Mimics can automatically generate the contours (or polylines) of a segmentation mask. These polylines
can then be used to fill in a masks cavities or to fit freeform CAD objects, like surfaces or spheres, to a
mask. The CAD objects created in Mimics can be directly exported as IGES files to any CAD program.

Scenario: As an engineer you need to design a standard implant for a partial knee replacement.
Before any design work can be done, the data from the CT scans must be imported into CAD. Use
Mimics to create an IGES surface, which can be exported to CAD, to relay all the information necessary
to begin the implant design. Follow the procedures in the step by step section to learn how to perform
these steps.
IGES Surfaces
Export to CAD requires an IGES file. Mimics creates an STL surface mesh, but traditional CAD packages
require a parametric surface file such as IGES. The MedCAD module allows us to create IGES surfaces
and curves based on the anatomical geometry from the scan.
1. Open up the knee_se.mcs
dataset.
2. Create a mask for the bones
using lower and upper
threshold values of 120 and
3071.
3. Crop the mask so it only
contains the upper portion of
the patients right knee (the
right femur).
4. Select region grow and click

somewhere on the right femur
to get rid of extra pixels in the
mask. Name the new mask
knee-1.
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5. Calculate a 3D model of knee1on high quality. You will
notice a lot of holes in the
mask which means editing
must be done.
6. Under Segmentation in the main toolbar click Calculate Polylines

mask and click OK.
. Select the knee-1
When Mimics calculates polylines it creates a contour around the selected mask on each slice. The
polyline set you just created will show up in the Polylines tab of project management.
7. Click on Cavity Fill from
Polylines
under
Segmentation in the main
toolbar. Make sure Fill Cavity of:
Set 1 and Using Mask: <New
Mask> are selected.
8. Click Apply and then Close.
Name the new mask knee-2.
Cavity Fill from Polylines is useful when a mask has many small holes that need to be filled in. On
each slice, this tool fills in all small holes of a mask that are encompassed by a larger boundary polyline.
9. Click on the eyeglasses in the project management Masks tab under the Visible column for all
of the masks except knee-2.
This turns off the masks so that they are not displayed in the images.
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10. Zoom in on the left knee in the axial
view. Starting at axial slice 0, scroll
up through the slices looking for
breaks in the knee-2 mask. You will
notice the first break on slice 57.
Make sure the knee-2 mask is active.

11. Go to Edit Masks and select Draw.
12. Draw in a connection where there is
a break in the mask.
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13. Scroll down through the slices
continuing to fill in any breaks until
you reach the end of the knee-2
mask. (Breaks also occur on slices
147, 132, 129, 123, 120, 117, 114,
111, and 108)
14. Under Segmentation in the main toolbar click Calculate Polylines

mask and click OK.
. Select the knee-2
Now that all the breaks have been filled in, calculating a new set of polylines will create contours that
include all the areas you just edited.
15. Select Cavity Fill from Polylines
. You want Fill Cavity of: Set 2 and Using Mask: <New
Mask>. Rename this mask knee-3.
All of the holes within the mask should be filled. If the holes are not filled then you missed a break
somewhere in the mask. In this case, go to the slice where there is still a hole. Draw in a connection on
the most recent mask using Edit Masks. Update the polylines by clicking Update Polylines
under
Segmentation (or use the shortcut CTRL + u). A dialog box will appear saying there are no polylines
created for the current mask and asks if you want to create them. Click Yes. Perform another cavity fill
from polylines but select knee-3 for Using mask:. Now, the break should be filled in.
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16. Calculate a 3D model on high
quality. Notice that this 3D model is
much more complete than the first
one calculated.
Since we are only going to look at the femur, we can use editing to erase the knee cap and the remaining
portion of the tibia.
17. Delete the kneecap, which can be
seen in axial slices 168 through 114,
using the green down arrow of Copy
to slices in Multiple Slice Edit
. You may need to select more
of the kneecap as you copy to each
slice.
Now the knee-3 mask should no longer contain the kneecap.

18. Use Erase of Edit Masks to erase
the extra area of bone from the
tibia on axial slices 108 and 105,
as well as any other slices that you
may have included when you
cropped the mask.
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19. Do a Region Grow and name the
new mask knee-4. Next, calculate
a 3D model. You should no
longer see the kneecap or extra
bone from the tibia.
20. Select Calculate Polylines. Click

on the knee-4 mask and then
press OK. Name this polyline set
polyKnee.
21. Click Polyline Grow
under
the Polylines project management
tab. Select From: polyKnee and
To: New Set. Check Auto multiselect, Keep Originals and set
Correlation(%) to 97.
Polyline Grow looks at polylines above and below the selected slice. If the polylines shape is within the
correlation percentages limits (within 97% similar), the polylines are automatically added to the current
polyline selection. A polyline selection is a portion of a polyline set.
22. Start at axial slice 207 and click on
the outer contour of the knee-4
mask. The contour will be
highlighted when you place your
mouse over it. You can also drag
a box around the knee.
23. Scroll upwards until you get to a

slice where you need to reselect
which polyline you want to grow
(slice 159). Continue reselecting,
as needed, up through axial slice
111 (you will need to reselect on at
least slices 156, 150, and 147 and
maybe more).
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24. Use Erase of Edit Mask to break
the connection on axial slice 96.
We must break this connection so that later

when we are growing polylines, we can
add an additional contour to the polyline
set. In order to be able to add a polyline,
the shape must resemble the previous
contour. If we did not do this editing there
would be a gap as shown in the picture on
the right.
25. While on slice 111, select Update Polylines
under Segmentation.
26. Select Grow Polylines with From:

polyKnee and To: New Set. On
axial slices 111, 108, and 105 select
the right most contour.
27. Select Grow Polylines with From:

polyKnee and To: New Set. On
axial slices 111, 108, and 105 select
the left most contour.
Now we have three polyline selections that are suitable for fitting a surface on. We need to turn these
separate contours into one surface because an IGES curve cannot be fit to multiple contours.
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28. In the main toolbar under MedCAD,
click Freeform Surface then click Fit
from Polylines. Select the first set
under the polyKnee set (Selection 5
in the picture on the right however
your number may be different).
Make sure you have at least 30
control points and click OK.
The u-parameters and v-parameters are automatically calculated for you. If the set contains more than
one contour per slice a surface cannot be fit. Also, you need at least three contours in a set to fit a
surface on. You will know if a set is good to fit a surface on because the Surface Fit Parameters box will
say Set OK.
29. Repeat this procedure for the last
two selections in the Polyline set
list. Look at the 3D view to see how
these selections look as surfaces.
30. Save this file as IGES Knee.
There are some holes in the surface at the top of the knee but the overall anatomical shape is correct.
These holes can be stitched and filled in CAD to create a solid part.
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Export to CAD
The surface created in the above exercise can be exported to CAD.
1. Select Export in the main toolbar, then click IGES.
2. Click the CAD tab
and highlight
surfaces 1, 2, and 3.
Press Add.
3. Select an Output
Directory. Click
Finish to export the
surfaces.
Homework 5
Open the hip_se.mcs dataset and create IGES surfaces for the femoral shaft, greater trochanter, and
femoral head.
Hint: Youll need to break the connection between the femoral head and greater trochanter to be able to
add polylines. Remember, polylines must be added to correct unwanted gaps that would otherwise exist.
You will also need to add a contour on the top of the greater trochanter so that youll have enough
contours in the set to fit a surface.
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Mimics Lesson 6: Centerline creation

Tools to learn: Calculate centerline, export centerlines to CAD, centerline measurements, cut
centerline ending.
Explanation
Mimics allows for the determination of centerlines for any type of branching including arteries, veins, and
airways. Tools exist to gather data about these centerlines such as maximum and minimum best fit
diameter, curvature, tortuosity, and hydraulic diameter. Centerlines can be modified within Mimics to
optimize the inlets and outlets for various analyses like CFD.

Scenario: As an engineer designing a stent, you need to analyze fluid flow through the aorta. Use
Mimics to calculate the centerline of the aorta and prepare the endings of the centerline for CFD. The
procedures outlined below will show you how to accomplish these tasks.
Calculate and Export Centerline

You can find the centerlines of veins and arteries, take measurements based on these centerlines, and
export the corresponding values.
1. Open the hip_se.mcs
dataset.
2. Perform a threshold with
values 174 to 279 and then a
region grow on the aorta.
(Axial slice 335 shown)
3. Name the mask Centerline and create a high quality 3D model.
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4. Select Fit Centerline under
Freeform Tree in the
MedCAD section of the
main toolbar.
5. Highlight the mask of the 3D
model of the artery. Leave
the default fitting parameters
and click OK.
Resolving resolution is the minimum detail you want Mimics to use in its centerline calculation. All of the
vessels in this dataset are bigger than 1 mm so we will leave the default value. Number of iterations is the
amount of times you want the algorithm to run. This is 2 by default, which is fine in most cases. Distance
between control points sets the distance between each point of calculation along the vasculature.
6. To better visualize the
centerline click on the
transparency button
the 3D toolbar.
in
The red dots on the centerline indicate bifurcation points.
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7. Select the CAD Objects tab
in the project management
toolbar and click Properties
.
The properties dialog box contains information about the centerline and its branches. Besides changing
the color of the centerline you also have the option to delete branches. To change which branches are
visualized, click on the eyeglasses of whichever branches you want to hide.
8. Highlight all of the branches by holding the control key while selecting each branch. Click
Export.
9. Click the yellow folder
to select an output directory. Name the file Aorta centerlines.
10. Select Text File (*.txt) for Save as type:.

You can export to a text file or as an IGES. The text file contains the coordinates of the points and the
selected measurements. These can be exported to programs such as Excel or Matlab for further analysis
depending on the application. To export to IGES select IGES under Export in the main toolbar and
select what you want to export under the CAD tab.
11. Leave only Best fitted diameter checked and click Save.
To see a definition for each of these measurements see the Centerline Measurements section of the
MedCAD menu help files.
Another way to take measurements is through New
Measurements project management tab.
12. Go to the Measurements tab and click
New
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The bottom half of the list deals with centerline measurements.
13. Select one of these measurements and put your mouse over the 3D model of the centerline to
see the measurements value. Repeat this for a few of the measurements.
As you move your mouse along the centerline, the values are updated for the measurement until you click
on a point.
Cut Centerline Ending

Cut Centerline Ending allows you to cut an end of a centerline perpendicular to the centerline in order
to create the flat inlet and outlet surfaces needed for CFD analyses.
1. Go to Actions
of the CAD Objects project measurement tab.
2. Select Cut Centerline Ending
3. Highlight Centerline 1
and click Indicate. On
the 3D model, click on
the top branch of the
artery to make a cut.
4. Click OK.
5. Make a few cuts on
different branches to
get familiar with the
tool.
The 3D objects tab will have the modified centerline (displaying how it looks with the cuts).
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Modify Centerline
Modify Centerline provides the ability to reposition centerline control points. This is useful when the
calculated centerline does not follow the accurate branching of a vessel and needs to be adjusted.
1.
Go to the CAD Objects menu. Select

the Actions button
and then Edit
Centerline Control Points.
You can modify a centerline by moving the control points.

2.
Select a control point you wish to

change. It will turn green.
3.
Next, select two control points on either

side of the green control point to
indicate the boundaries of your change.
These will turn black.
4.
Drag the green control point to the desired location until it is in the position that you want.
Double-click to finalize the change.
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Notice that now the centerline has less curvature than it did originally.
Homework 6
Using the heart_se.mcs dataset, segment some of the pulmonary branches coming off of the heart.
Choose one of the branches and find the following at a few different points along the branch:
1. Best fit diameter
2. Maximal and minimal diameters
3. Tortuosity
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Mimics Lesson 7: FEA (part 1)

Tools to learn: Remeshing, creating a volume mesh, material assignment, export to FEA.
Explanation
The FEA module of Mimics allows optimization of triangle meshes to prepare for further analysis using
FEA or CFD. Remeshing is used to increase and optimize the quality of triangles and preprocess a
model for analytical packages. The typical process for remeshing includes smoothing the mesh to
remove sharp edges that may act as unwanted stress risers in analysis, reducing the number of triangles
to enhance the calculation speed during FEA, and optimizing triangle quality. The following picture shows
an example of a mesh before and after it has been optimized.
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The Mimics remesher is broken up into a few main windows; these include the log window, the 3D view,
the database and inspection page section, and the operations and properties section. A list of all the
steps and operations you complete is available in the log window. The 3D view allows you to see the 3D
model of the part you are working on. The tab next to 3D view, the inspection scene, is where you can
visualize the triangulated mesh corresponding to your part.
The upper right box includes the database and inspection page. The database page gives you
information about each part, surface, curve, and sketch created. You can use the database tree to select
various objects for a specific operation. The inspection page allows you to control all your remesh
operations and to inspect and visualize the quality of your mesh.
The properties page will show you all properties (such as number of triangles, color, volume, surface area,
etc.) associated with a selected object. The operations page shows all the parameters available to
change when applying an operation to your object. As an example, the operations page for the smooth
tool is shown below.
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Once FEA meshes are created, Mimics can assign material properties based on Hounsfield units and
export to FEA packages directly. The ability to assign material properties comes from the close
correlation between the density of a CT image and the density of anatomical materials, like bone.

Scenario: You are asked to perform finite element analysis to explore the biomechanics associated
with the joint at the hip. Prepare the femoral head for FEA using the Mimics remesher and then assign
material properties to your mesh based on the gray value information in the CT scan. The procedures
outlined below will show you how to accomplish these tasks.
Preparing a Mesh for FEA
Recall the typical remeshing protocol discussed in the explanation section:
1. Smooth mesh to remove sharp edges which may act as unwanted stress
risers in FEA
Use Smooth
tool
2. Reduce the number of triangles to enhance calculation speed during FEA

Use Reduce
and Quality Preserving Reduce Triangles
3. Optimize meshs triangle quality

Use Auto Remesh
Remeshing
Remeshing is used to increase and optimize the quality of triangles for the preprocessors of analytical
packages.
1. Open up the FEA_femur_se.mcs project.
2. Highlight the Femur in the 3D Objects tab of the project management toolbar.
3. Click the Remesh
button in the same tab.
Model navigation works the same in the remesher as in normal Mimics.

4. Go to the Remeshing tab
located at the top of the
Remesher.
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5. Click the Smooth button
and then click on the 3D model of the femur. Select Femur.
6. Leave the smoothing parameters at the default settings. Check Preserve sharp edges under
Advanced Options and click Apply.
In order to prevent the bottom of the femur from being rounded we must check preserve sharp edges.
The higher the smooth factor the more smoothing will be applied, with a value of 1 applying the most
smoothing. Number of iterations is the amount of times the smoothing algorithm will be applied. We use
compensation to counteract any shrinking that might occur as a result of the smoothing algorithm.
7. Select the Reduce button
in the
Remeshing tab and click on the part
selecting Femur.
8. Change Geometrical error to 0.09 and
leave the rest of the default reducing
parameters. Leave preserve surface
contours unchecked. Click Apply.
If during the process of reducing, 2 triangles are replaced by one triangle, it may be that there is a small
amount of deviation in position. Geometrical error is the maximum deviation allowed between the original
surface and the new one. It is recommended to use 1/8 of the pixel size to maintain accuracy between
scanner data and models, so in our case the datasets pixel size of 0.715 mm translates to a geometrical
error of about 0.09.
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Flip threshold angle specifies the maximum angle that is allowed between two triangles during smoothing.
Preserve surface contours should be used when there are surfaces defined that are not based on the part
geometry.
9. Click Auto Remesh
in the Remeshing tab and make sure part is selected for Entities.
10. Select Height/Base (N) for

Shape Measure in the
Inspection Page tab. Change
the minimum and maximum
values to 0 and 0.3.
Auto remesh removes groups of small triangles that are still contained in the mesh. You can visualize
shape measure on the histogram by changing Current Measure to Shape Measure under Histogram
Parameters. The histogram is measuring the quality of all triangles in the mesh. We want all of the
triangles to be above the 0.3 shape measure threshold we set because triangles with a quality lower than
this will not import into FEA or CFD packages.
11. Change the Maximum
geometrical error to 0.4, check
Control triangle edge length,
and set Maximal edge length
to 5. Leave the rest of the
default parameters and click
Apply.
A rule of thumb is to keep the geometrical error used in reducing the same as the maximum geometrical
error. With this example, we have the flexibility to increase the maximum geometrical error to 0.4 so we
can increase computation time by reducing the number of triangles. Some of the auto remesh parameters
include shape quality threshold which sets the desired quality of triangles, maximum geometrical error
which is the maximum deviation between the parts surface before and after automatic remeshing, and
maximal edge length which sets a limit on the length of edges of triangles created. Large models with
many low quality triangles can be better remeshed in incremental steps; sometimes it helps to use a
shape quality threshold of 0.1, then 0.2, and then 0.3.
12. Click Quality Preserving Reduce Triangles
in the Remeshing tab then click on the part.
This step further reduces the amount of triangles while preserving the quality.
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13. Check Control triangle edge
length, set the Maximal edge
length to 5, and leave the rest
of the default parameters. Click
Apply.
Your model should resemble the femur in the picture shown above. The Remesh Wizard
can be
used to achieve nearly the same results as the steps weve done so far. With this tool the software
determines the parameters automatically; however, manually performing the steps allows more control
over the parameters.
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Material Assignment
Mimics assigns materials to volumetric meshes based on Hounsfield gray values. You can create a
volume mesh in the remesher, bring the volume mesh back into Mimics and then assign material
properties.
1. Duplicate the Femur by
right-clicking and selecting
Duplicate under the Active
Scene tab.
This allows us to have a surface mesh and a volume mesh when we go back into Mimics. If you wanted
to load a mesh rather than create one, you would click Load Mesh
project management.
2. Select Create Volume Mesh
under the FEA Mesh tab of
in the Remeshing tab.
3. Make sure Femur is selected as Entity.

Set Method to Init and Refine, Shape
measure to Aspect ratio (A), and Shape
quality threshold to 25.
4. Click Apply.
The mesh parameters allow you to define certain details of your mesh. For example, the method used to
create the tetrahedral volume mesh can either fill the volume, as with Init, or fill the volume and fit the
tetrahedral elements more appropriately, with Init and Refine. Control edge length limits the tetrahedral
elements to the dimension you set. The analyze mesh quality options define how Mimics analyzes the
mesh. Aspect ratio is a common mesh analysis for FEA. It is good to set the shape quality threshold to at
least 25 when using aspect ratio, since thresholds below this are considered poor quality and not
accepted by most FEA packages.
5. To view the elements in the volume
mesh, first select the 3DView tab. Next,
go to the Active Scene tab and under
3DView expand the Section List.
6. Right-click Standard Section Y and
then click Show.
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7. In the Standard Section Y tab, turn on
clipping. Move the slider next to Position
to observe the volume mesh in the 3D
view.
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8. Close the remesher to return to Mimics by
clicking the
corner.
in the upper right-hand
The surface mesh can be found in the 3D Objects tab and its name will start with the word Remeshed.
The volume mesh can be found in the FEA Mesh tab.
9. Turn on only the volume mesh
in the 3D pane.
10. Click the glasses under
Contour Visible in the FEA
Mesh tab to view where the
mesh is located in 2D.
11. Click Enable/disable clipping

. In the Clipping tab, check
the Axial and Sagittal boxes
under Active. Set the
Texturing to None for both.
Scroll through the 2D axial and
sagittal views to visualize the
internal distribution of the
mesh.
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12. Press the Materials
icon.
13. Click Yes to the dialog box

that pops up.
This message explains that Mimics needs time to calculate the average gray value for the pixels of each
element of the mesh.
14. Make sure Uniform is
selected under Method
and set the number of
materials to 15. Leave
Limit to Mask: None.
The uniform method divides the range of gray values

into equal sized intervals based on the number of
materials you picked. Selecting Materials under the
Histogram tab allows you to preview these intervals.
The look-up file method uses an existing file with
predefined gray value intervals to assign materials.
The mask method takes masks you created in the
project and assigns one material per selected mask.
Experiment with the different options to familiarize
yourself with the different methods of material
assignment.
15. Click on the Material Editor tab.

This is where you can enter properties for materials such as density. In the Use material expressions
section you can manually enter known expressions for properties. A list of such expressions can be
found in the help files by clicking the contents tab> Mimics Modules> FEA> Empirical Expressions.
16. Select OK.
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17. Enable clipping in only
the coronal view and set
Texture to None.
Scroll through the
coronal view to see the
internal material
distribution.
Export to FEA
Meshes created or modified in Mimics can be exported for further analysis in FEA packages.
1. Click Export Mesh
in the FEA Mesh tab.
You would select the name of the mesh you want to export under the Mesh tab, select an output format,
click Add, and then select OK.
2. Click Cancel.
Homework 7
Open the knee_hw_se.mcs file and complete the following:
1. Following the same procedure used to remesh the femoral head, create a refined surface mesh of
the distal femur. Compare the number of triangles in the model before and after remeshing.
2. Calculate the volume mesh for the model. Display the volume element contours over the CT
images to verify that the model accurately represents the distal femur.
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Mimics Lesson 8: FEA (part 2)

Tools to learn: Wrap, create and split a non-manifold assembly, create volume mesh.
Explanation
When running an FE analysis on multiple parts, mating parts need node to node matching. To
accomplish this, the FEA module of Mimics can generate non-manifold assemblies, or t-sections. Nonmanifold assemblies create matching surfaces between parts such as between bone and implant. Once
an assembly is created the entire mesh can be optimized for FEA in the remesher. After remeshing is
complete, you can split the bone and implant mesh into two separate meshes using the splitting tool. This
final step creates the two separate meshes with a node to node matched surface.
If a volume mesh is needed for FEA, the Create Volume Mesh tool can be used to generate a volume
mesh of the non-manifold entities that were split.

Scenario: You would like to research the stresses associated with a jaw implant using FEA. You first
want to analyze the implant and bone as a single mesh and then later as two separate meshes. Use
Mimics to create these meshes. The procedures outlined below will show you how to accomplish these
tasks.
Non-Manifold Assembly
Creating a Non-Manifold Assembly
Non-manifold assemblies are created to make sure the common surface between parts, like between an
implant and bone, is identical. This is necessary to perform accurate FEA.
1. Open the skull_se.mcs project.
2. Perform a threshold and region grow to
segment the mandible. Name the mask
Mandible.
3. Calculate a 3D model.
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4. Use Edit Mask in 3D to remove the
second from the last molar on the patients
left side of the jaw, also called the lower left
first molar. Remember to do a region grow
and recalculate the 3D model after you are
finished editing.
5. Turn on the tooth_implant STL.

6. Reposition the implant using the Simulation
module so that it fits into the socket where
you removed the tooth. Make sure to place
the implant so that the tooth portion
intersects slightly with the gums (see
picture on right).
Later, when we are creating a volume mesh of the non-manifold assembly, we dont want to run into the
problem of having overlapping triangles that prevent us from being able to calculate a volume mesh.
Moving the implant farther down into the gums accounts for this.
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7. Turn on Clipping
in the 3D Toolbar.
8. In the Clipping tab of project

management, check the box next to
Sagittal under the Active column.
9. Change the Texturing to None by clicking
on the word under the texturing column
until it says None.
10. Scroll through the 2D sagittal images and

notice that in the 3D view there are some
holes in the model.
11. Turn off Clipping.
The Wrap
tool in the Remesher can be used to fill in the holes of the 3D model. This is an especially
useful tool for FEA where holes can cause inaccurate results.
12. Choose Remesh under the FEA/CFD menu in the main toolbar.
13. Select both the tooth implant and the mandible with the removed tooth by pressing the CTRL key
while selecting the parts, then click OK.
14. Go to the 3D View tab in the remesher.
15. Select Wrap
in the Fixing tab.
16. Select Mandible and tooth_implant as

Entities.
17. Set Gap closing distance to 0.2 and
Smallest detail to 1. Leave the rest of the
default parameters. Click Apply.
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Gap closing distance determines the size of gaps that will be wrapped. Smallest detail sets the size of
the triangles of the newly created surface. Check the help files for details on the other wrap parameters.
18. In the Active Scene tab, right-click the
Mandible and select Hide.
19. Repeat this for the tooth_implant so that
only the wrapped 3D models are displayed
in the 3D view.
20. Click the plus sign next to Section List in

the Active Scene tab and then click
Standard Section-X.
21. In the Standard Section-X tab, check the
box next to Clip to enable clipping.
22. Click Position and a scrollbar will appear.
Move the scrollbar and check the 3D view
to ensure all holes have been filled in from
the wrap.
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The wrapped model should contain no holes in the locations where the original model did. Now we can
create a non-manifold assembly.
23. In the Remeshing tab click Create non-manifold assembly
24. Left-click on the Mandiblewrapped to select it as the

main entity. Click on
Intersecting entity then leftclick the
tooth_implant_wrapped.
25. Click Apply to combine the mandible and implant meshes.

26. Choose the Create Inspection Scene tool
under the Remeshing tab.
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27. Select the
Mandible_wrapped_nonmanifold_assembly for
Entity in the create
inspection scene tab. This
can also be selected from
the database tree.
28. Click Apply.
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Optimizing the Non-Manifold Assembly Mesh

We want to create an optimized mesh just as we did for FEA remeshing.
1. Click the Filter Sharp Triangles tool
in the Fixing tab. Left click on the 3D model and select
Mandible_wrapped_non-manifold_assembly.
Sharp triangles must be removed because they are detrimental to the quality and speed of FEA.
2. Set the Filter small triangles
parameters to Filter distance:
0.2000, Threshold angle:
15.000, and Filter mode:
Collapse. Click Apply.
3. Select Smooth
Since the 3D model will only be used for FEA you can reduce the amount of detail of its outer surface by
smoothing.
4. Left click on the 3D model and
select the Mandible_wrapped
_non-manifold_assemblys
Surface. Check Preserve
sharp edges under Advanced
options and leave the rest of the
default parameters. Click Apply.
5. Click Reduce
then left click on the 3D model to select Mandible_wrapped_nonmanifold_assembly.
There are too many triangles for Finite Element Analysis so a reduction is necessary.
6. Set the Flip threshold angle to 30,
Geometrical error to 0.06 and check
Preserve surface contours. Leave
the other parameters at the default
settings and click Apply.
7. In the Inspection Page tab, select Height/Base (N) in the Shape measure dropdown under
Quality parameters.
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8. Make sure the slider on the
histogram is at 0.3, the quality
needed to generate a volume
mesh.
9. Make sure Shape Measure is selected for Current measure in Histogram parameters. Click
Auto Remesh
10. Set the Maximum geometrical

error to 0.1 and uncheck Control
triangle edge length. Leave the
other parameters at the default
settings. Click Apply.
11. Apply auto remesh again after

checking Control triangle edge
length. Leave the other
parameters the same.
Since the first auto remesh left the mesh containing triangles of divergent sizes, if we limit the maximum
edge length we can create a uniform mesh.
12. Click Quality Preserving
Reduce Triangles
in the
Remeshing tab. Change the
Maximum geometrical error to
0.2 and leave the other default
parameters.
Quality preserving reduce triangles removes the groups of small triangles still contained in the mesh.
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13. Click Apply. The final result is a
uniform mesh with the desired
quality.
Splitting a Non-Manifold Assembly and Exporting the Remeshed Parts

This tool will take the combined jaw and implant mesh we created above and separate it into one
mesh for the implant and one for the jaw with node to node matching on mating surfaces.
1. Select the Split non-manifold assembly tool
2. Go to the 3D view and select the Mandible_wrapped_non-manifold_assembly for Entities.

3. Click Apply.
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Creating a Volume Mesh for a Non-Manifold Assembly

Volume meshes can be created for the parts resulting from the split non-manifold assembly.
1. In the Remeshing tab select the Create Volume Mesh tool
2. Select the mandible as your entity and Init and Refine as Method. Choose Aspect Ratio for
Shape measure and set the Shape quality measure to 25.
3. Repeat the process of creating a volume mesh for the tooth implant.
If we did not position the implant to account for overlap in step 6 of the Creating Non-Manifold
Assembly section, the create volume mesh tool may have resulted in an error of overlapping triangles.
The non-manifold assembly algorithm requires a certain amount of overlap to produce high-quality
results. Otherwise, in certain cases the algorithm can produce triangles that cause problems during
volume meshing. In the example below, the overlap in Figure 1 would potentially cause errors;
whereas the overlap in Figure 2 is better.
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4. Exit the remesher to return to Mimics.

The remeshed 3D objects can be exported using the Export menu if needed.
Homework 8
Using the knee_hw_se.mcs dataset, complete the following:
1. Create a non-manifold assembly of the distal femur and knee_implant STL.
2. Remesh the assembly to achieve a quality threshold of 0.3. Display the surface mesh with the
Color low quality triangles option checked. Do you think the overall quality of this mesh is better
or worse than the refined mesh from HW 7? Why?
Hint: Change your auto-remesh parameters for geometrical error to 0.08 and maximum edge
length to 10. Depending on your computer, the analysis may take several minutes to complete.
3. Split the assembly back into separate parts and exit the remesher. Click the Contour Visible
eyeglasses in the 3D Objects tab to show the position of the femur and implant models in relation
to the CT images. Scroll through several of the images and verify that the models still accurately
represent the patients anatomy.
Hint: Visualizing the model contours may be easier if you change the 3D part colors.
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Mimics Final Project

All of the datasets you have previously worked in this course with have been CT scans; however, working
with MRI data is different than working with CT. In MRI, bone shows up as black and soft tissue shows up
as shades of gray. This imaging modality can be very useful for segmenting separate soft tissue
structures, which may be difficult to distinguish in CT images. Think about what tools are affected by this
change in gray scale mapping.
Open the MRI dataset called MR_brain_se.mcs. See how many regions of the brain you can make 3D
models of (i.e. the cerebellum, cerebrum, brain stem, etc.)
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Congratulations!
You now know how to utilize the tools in Mimics to transform 2D data into 3D models. Thank you for using
the Mimics Student Edition for your learning experience. If you would like more information about any of
the Materialise software please contact us at:
Materialise
44650 Helm Court
Plymouth, MI 48170
www.materialise.com
mimics@materialise.com
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Need help? Check out the Mimics User Community at http://uc.materialise.com/mimics/
Refer to first
page to activate
SE
Mimics
Need help? Check out the Mimics User Community at http://uc.materialise.com/mimics/

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Mimics Student Edition Course Book v13.1

2. In the Password Request Wizard, Select Add a server.

4. Click Next twice followed by Finish to finish activating the account.

Activating MimicsSE ................................................................................................. i

Lesson 1: Mimics Navigation ................................................................................ 8

Measurement Tools ...........................................................................................................15

Mimics Lesson 2: Basic Segmentation .............................................................. 17

Mimics Lesson 3: Advanced Segmentation ....................................................... 29

Mimics Lesson 4: Surgical Simulation ............................................................... 40

Mimics Lesson 5: CAD export ............................................................................. 45

Mimics Lesson 6: Centerline creation ................................................................ 54

Mimics Lesson 7: FEA (part 1) ............................................................................ 60

Mimics Lesson 8: FEA (part 2) ............................................................................ 71

Mimics Final Project ............................................................................................. 82

From image to model

STL file explanation

Figure 1. Triangulation of an STL file.

Figure 2. Editing a Mimics model in 3D to capture only the femoral head.

Figure 3. 3D objects calculated from CT images.

Rapid Prototyping (RP)

Figure 4. Mimics models printed on an RP machine with support generation.

Figure 6. Original mesh of two parts without node-to-node matching.

Figure 9. Surgical simulation of the placement of a femoral implant.

Discussion and Conclusion

Before You Start

How to Use this Tutorial

Phrases in bold represent tools in Mimics.

Lesson 1: Mimics Navigation

Step by Step Tutorial

3. Select the Unzoom tool

and click on the same image you just zoomed in on.

4. To create a full screen view, select Zoom to Full Screen

3. Click on the Context Help icon

1. Change the contrast of the

under Measurements in the main

2. Click once on one side of

and then select Measure Angle

Other Useful Tools

4. Next click the image near the

Mimics Lesson 2: Basic Segmentation

Step by Step Tutorial

3. Click through the predefined

Thresholding with Draw Profile Line

2. Select Draw Profile Line

3. Click once below the femur to start the

5. Click Start thresholding in the

1. Select Region Growing

from the Segmentation toolbar. The mouse will turn cross-shaped.

2. Select Source (= BoneThreshold) and Target mask

3. Enter the following

2. Click Edit Masks

under Segmentation and select Erase in the Edit Masks toolbar.

Dynamic Region Grow

4. Calculate a 3D model of this mask on

3. In the same tab,

also in the 3D toolbar.

9. Scroll through the axial view to move the clipping plane.

Mimics Lesson 3: Advanced Segmentation

Step by Step Tutorial

Multiple Slice Edit

in the project management Mask tab.

5. Under Segmentation in the main toolbar click Multiple Slice Edit