Mimics Student Edition Course Book

Mimics Student Edition Course Book v13.1

SE

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Need help? Check out the Mimics User Community at http://uc.materialise.com/mimics/

/ 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 “Password Request” and then click “Next”.

2. Enter your email address and the CCK code provided by your professor. Click “Next”.

3. Click “Finish” to open the Materialise Web Password Generation website.

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4. Choose the appropriate country flag to set the language.

5. Choose your name from the drop-down list or select “Add Contact Person” if your name is not yet in the list. Next, click “Password Generation”.

6. All appropriate fields will be filled in. Click on “Request Password” and an email will be sent to

the email account on file.

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7. Once you receive an email with your password go back to the Password Request Wizard. Select “Enter Password.”

8. Copy the password that was emailed to you into the “Enter Password” space and then click “Next”.

9. Your registration is now complete. Click “Finish”.

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/ Table of Contents / Activating MimicsSE ................................................................................................. i / Table of Contents .................................................................................................. iv / 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 Step by Step Tutorial .........................................................................................................18

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

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/ Mimics Lesson 3: Advanced Segmentation ....................................................... 29 Explanation ........................................................................................................................29 Step by Step Tutorial .........................................................................................................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


Scenario: ......................................................................................................................................... 40 Cut .................................................................................................................................................. 40 Import and Reposition an STL ........................................................................................................ 43

Homework 4 ......................................................................................................................44 / Mimics Lesson 5: CAD export ............................................................................. 45


Scenario: ......................................................................................................................................... 45 IGES Surfaces ................................................................................................................................ 45 Export to CAD ................................................................................................................................. 53

Homework 5 ......................................................................................................................53 / Mimics Lesson 6: Centerline creation ................................................................ 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


Scenario: ......................................................................................................................................... 62 Remeshing ...................................................................................................................................... 62 Material Assignment ....................................................................................................................... 66 Export to FEA ................................................................................................................................. 70

Homework 7 ......................................................................................................................70 / Mimics Lesson 8: FEA (part 2) ............................................................................ 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 / Mimics Final Project ............................................................................................. 82 / Congratulations! ................................................................................................... 83

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/ Introduction Mimics (Materialise's Interactive Medical Image Control System) is Materialise’s 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 world’s 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 Materialise’s 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 Materialise’s 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. 3-matic is Materialise’s 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 didn’t 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. Materialise’s 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 Materialise’s 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 CAE-ready 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 Mimics or within a 3

rd 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 design’s 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

Make sure to install the Anthropometry and Distractor libraries which can be found on the MimicsSE 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.

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.

Axial

Coronal

Sagittal

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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 slice’s 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 patient’s 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 in

the 3D toolbar.

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 under ‘Measurements’ in the main

toolbar.

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 angle’s

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 annotation’s 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 point’s 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

patient’s 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 patient’s 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 “Bone-

Threshold” 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.

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5. Click ‘Start thresholding’ in the

‘Profile Lines’ dialog box.

6. Hit ‘Apply’ in the thresholding

dialog box since we are

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 (= Bone-

Threshold)’ 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.

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5. Repeat the procedure

for region growing on

the ‘Bone-Profile line’

mask. Name the new

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 ‘Bone2-

threshold’ 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’.

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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 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 ‘Bone2-

Threshold’ 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).

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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

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 in the

‘3D objects’ project

management tab.

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

Aorta’s 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 object’s 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 patient’s head is not included in this mask. 2. Mandible 3. All bone, including the mandible. (Optional) 4. Export a short movie showing the models you’ve 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 aorta’s 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 in the project management ‘Mask’ tab.

Rename the cyan mask ‘Spine’.

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 8. 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 3D.

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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 low-contrast 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 . Rename

the new mask “Aorta-interpolate”.

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 8-

connectivity. 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 patient’s stent, use Edit Mask in 3D to get rid

of the protrusions and then recalculate the 3D model.

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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 and then Measure

Distance Over Surface.

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.

40


/ 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 patient’s 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 patient’s 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 ‘PolyplaneCut-

Mandible’ 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 Cut-

Mandible’ 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 mask’s 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 patient’s right knee (the

right femur).

4. Select region grow and click

somewhere on the left 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 ‘knee-

1’on 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 . Select the ‘knee-1’

mask and click ‘OK’.

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 . Select the ‘knee-2’

mask and click ‘OK’.

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 multi-

select’, ‘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 percentage’s 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: You’ll 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 you’ll 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 in

the 3D toolbar.

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 in the ‘Measurements’ project management tab.

12. Go to the ‘Measurements’ tab and click

New .

The bottom half of the list deals with centerline measurements.

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13. Select one of these measurements and put your mouse over the 3D model of the centerline to

see the measurement’s 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 mesh’s 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’.

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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 dataset’s pixel size of 0.715 mm translates to a geometrical error of about 0.09.

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 part’s 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 we’ve 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 under the ‘FEA Mesh’ tab of project management.

2. Select Create Volume Mesh 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.


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 in the upper right-hand

corner.

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. Non-manifold 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 patient’s

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 don’t 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 ‘Mandible-

wrapped’ to select it as the

main entity. Click on

‘Intersecting entity’ then left-

click 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_non-

manifold_assembly’ for

‘Entity’ in the create

inspection scene tab. This

can also be selected from

the database tree.


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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 in the ‘Remeshing’ tab.

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_assembly’s

‘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_non-

manifold_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 in the ‘Remeshing’ tab.

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 in the ‘Remeshing’ tab.

2. Go to the 3D view and select the ‘Mandible_wrapped_non-manifold_assembly’ for ‘Entities’.


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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 patient’s 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 [email protected]

http://www.materialise.com/

mailto:[email protected]


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