Mimics Student Edition Course Book

Mimics Student Edition Course Book

SE

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Mimics Student Edition Course Book Mimics Student Edition Course Book .......................................................................... 1 / Introduction ............................................................................................................ 3 / Overview ................................................................................................................. 3

Materialise Overview ............................................................................................................. 3 Mimics history ...................................................................................................................... 3 From image to model ............................................................................................................ 3 STL file explanation ............................................................................................................... 3 Segmentation ....................................................................................................................... 4 The applications of Mimics ..................................................................................................... 5 RP ....................................................................................................................................... 5 CAE ..................................................................................................................................... 6 Remeshing ........................................................................................................................... 7 Volume Mesh ....................................................................................................................... 7 Material properties ............................................................................................................... 7 CAD ..................................................................................................................................... 8 Surgical Simulation ................................................................................................................ 8 Discussion and Conclusion ...................................................................................................... 9 Before You Start .................................................................................................................... 9

Install Libraries .................................................................................................................................. 9 How to Use this Tutorial.................................................................................................................... 9

/ Lesson 1: Mimics Navigation .............................................................................. 10 1.1 Explanation ..............................................................................................................10 1.2 Step by Step Tutorial .................................................................................................12

Scenario: ......................................................................................................................................... 12 Navigation ....................................................................................................................................... 12 Zooming and Panning ..................................................................................................................... 12 Shortcuts ......................................................................................................................................... 12 Help Pages ..................................................................................................................................... 13 Project Management ....................................................................................................................... 13 Project Management Toolbar ......................................................................................................... 13 Windowing ...................................................................................................................................... 14 Volume Rendering .......................................................................................................................... 15 Measurement Tools ........................................................................................................................ 15 Measurement Tools ........................................................................................................................ 15 Measure Density and Making Annotations ..................................................................................... 16

1.3 Homework ...............................................................................................................17

/ Mimics Lesson 2: Basic Segmentation .............................................................. 18 2.1 Explanation ............................................................................................................18 2.2 Step by Step Tutorial ..............................................................................................18

Scenario: ......................................................................................................................................... 18 Thresholding Toolbar ...................................................................................................................... 18 Thresholding with Draw Profile Line ............................................................................................... 19 Region Grow ................................................................................................................................... 20 Calculate 3D ................................................................................................................................... 22 Crop Mask ...................................................................................................................................... 23 Edit Mask ........................................................................................................................................ 24 Dynamic Region Grow .................................................................................................................... 26 3D Tools.......................................................................................................................................... 27 Capture Movie ................................................................................................................................ 29

2.3 Homework ..............................................................................................................30

/ Mimics Lesson 3: Advanced Segmentation ....................................................... 31

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3.1 Explanation ............................................................................................................31 3.2 Step by Step Tutorial ..............................................................................................31

Scenario: ......................................................................................................................................... 31 Multiple Slice Edit ........................................................................................................................... 31 Interpolate ....................................................................................................................................... 34 Edit Mask in 3D ............................................................................................................................... 36 Morphology Operations .................................................................................................................. 38 Boolean Operations ........................................................................................................................ 39 Measure Distances ......................................................................................................................... 40 Export to txt ..................................................................................................................................... 41

3.3 Homework ..............................................................................................................41 / Mimics Lesson 4: Surgical Simulation ............................................................... 42


Scenario: ......................................................................................................................................... 42 Cut .................................................................................................................................................. 42 Import and Reposition an STL ........................................................................................................ 45

4.3 Homework ..............................................................................................................46 / Mimics Lesson 5: CAD link .................................................................................. 47


Scenario: ......................................................................................................................................... 47 Iges Surfaces .................................................................................................................................. 47 Export to CAD ................................................................................................................................. 54

5.3 Homework ..............................................................................................................55 / Mimics Lesson 6: Centerline creation ................................................................ 56


Scenario: ......................................................................................................................................... 56 Calculate and Export Centerline ..................................................................................................... 56 Cut Centerline Ending ..................................................................................................................... 59 Modify Centerline ............................................................................................................................ 60

6.3 Homework ..............................................................................................................61 / Mimics Lesson 7: FEA (part 1) ............................................................................ 62


Scenario: ......................................................................................................................................... 64 Remeshing ...................................................................................................................................... 64 Material Assignment ....................................................................................................................... 67 Export to FEA ................................................................................................................................. 70

7.3 Homework ..............................................................................................................71 / Mimics Lesson 8: FEA (part 2) ............................................................................ 72


Scenario: ......................................................................................................................................... 72 Creating a Non-Manifold Assembly ................................................................................................ 72 Optimizing the Non-Manifold Assembly Mesh ................................................................................ 76 Splitting a Non-Manifold Assembly and Exporting the Remeshed Parts ....................................... 79

8.3 Homework ..............................................................................................................80

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/ Introduction Mimics (Materialise's Interactive Medical Image Control System) is Materialises software for processing medical images and creating 3D models. Mimics uses 2D cross-sectional medical images such as from computed tomography (CT) and magnetic resonance imaging (MRI) to construct 3D models, which can then be directly linked to rapid prototyping, CAD, surgical simulation and advanced engineering analysis.

/ Overview Materialise Overview Materialise is an international company, best known for its activities in the field of rapid, industrial, and medical prototyping. Started in 1990 as a spin off corporation from the University of Leuven in Belgium, it began as a rapid prototyping service bureau. Since then, Materialise has grown into the worlds largest rapid prototype producer. The company also enjoys a worldwide reputation as provider of innovative software solutions. As such, Materialise has acquired the position of market leader for 3D printing and digital CAD software in addition to being a major player in medical and dental image processing and surgery simulation. For the medical and rapid prototyping industries, Materialise offers an array of software solutions; Mimics is the medical image based processing tool for creating 3D models, and linking the models to rapid prototyping (RP), computer aided engineering (CAE), computer aided design (CAD), and surgery planning. SurgiCase CMF is Materialises CT based craniomaxillofacial surgical planning software. It allows users to import patient data, create 3D models, plan out the surgery, and rapid prototype surgical guides that can be used during the operation to match the surgical plan. SimPlant is Materialises dental implant planning software. Similar to SurgiCase, it allows users to plan dental implant surgeries and prepare surgical guides for the operating room. All medical software packages developed by Materialise are FDA approved. Magics RP is considered a powerful preprocessor for additive fabrication. It prepares 3D object (STL) files for additive fabrication as well as performs easy mesh and geometry manipulation. 3-matic is Materialises forward engineering software that allows advanced manipulation and design on an STL file. It allows a user to perform digital CAD operations (i.e. typical CAD operations on a STL file instead of the traditional CAD files), and fix and remesh for CAE. Materialise ensures that all software packages are ISO-9001 certified and that there is a seamless link between all packages.

Mimics history After the start of the company Materialise in 1990 as a rapid prototyping company, it didnt take long for the company to see the analogy between RP and CT (or MRI) images; in RP, a 3D model is built slice per slice, whereas a CT scanner does the reverse, it breaks down a 3D model (the human body) into a stack of image slices. In 1992 Materialise wrote software that linked the image information to RP models. The software allowed extracting 3D information from an image stack and building a 3D model from it, using RP technology. Materialises Interactive Medical Image Control System (MIMICS) was born.

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

STL file explanation An STL file is a triangulated surface mesh file. 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

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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. Below is an example of the 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 grayvalues (Hounsfield units in CT images) within these images. A grayvalue 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 grayvalue 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 grayvalues, 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), but Mimics also has a unique 3D editing tool; an initial segmentation can be optimized in a 3D preview (Figure 1). This makes editing very easy, since it allows true editing in 3D, which is easier to comprehend than 2D editing.

Figure 1. Editing a Mimics model in 3D to capture only the femoral head.

Using the segmentation and known information on the pixel size and the distance between the image slices, Mimics can calculate a 3D model (Figure 2). The accuracy in a Mimics model matches the accuracy of an object captured within the scan.

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Figure 2. 3D objects calculated from CT images.

The applications of Mimics Although Mimics was originally designed to link medical images to rapid prototyping, there are of course many applications possible using the 3D model that is calculated after segmentation. Over the years Mimics evolved to the Golden Standard in linking medical images to various applications. Continuous developments and the inclusion of new tools continue to widen the application base. The applications that will be discussed here in more detail are:

Rapid Prototyping (RP)

Computer Aided Engineering (CAE)

Computer Aided Design (CAD)

Surgical Simulation

All these applications require slightly different processing before they can effectively be used. Mimics development continuously strives to optimize this pre-processing to ensure a fluent workflow from images to application.

RP The 3D object created within Mimics is an STL file. STL is the common language for rapid prototyping machines and 3D printers and it can describe very complex geometries (like medical geometries). The 3D object can be directly exported to rapid prototyping in either STL or Sliced file format; in the latter it also allows support generation. Or it can be imported into Materialises Magics program for support generation or for build optimization. Figure 3 shows how models exported from Mimics were prepared in Magics to generate supports and duplicate the object to print multiple models at once.

Figure 3. Mimics models printed on a 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 good 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 in tiny, discrete elements and calculates the variables for every element. The magnitude of the variable is usually visualized with colormaps. 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 softwares require STL files that use equilateral triangles to describe the 3D. Figure 4 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 4. The difference between an STL file 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 analyse 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 analyse 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 seperate STL files as shown in figures 5, and 6.

Figure 5. Original mesh of two surfaces

without node-to-node matching.

Figure 6. 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 greyscale 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 grayvalues represent material density. This information is used in Mimics to accurately assign material properties to the elements of the volume mesh (Figure 7).

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Figure 7. Distributed material property assignment for an FEA analysis based on the grayvalues in a CT scan. Colored 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 link 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. 3-matic is described in more detail in chapter 3.5.1.

Surgical Simulation Mimics helps bridge the gap between clinicians and engineers. With Mimics surgical simulation functions, a surgery can be performed within the virtual world prior to entering an operating room (OR). Typical OR procedures can also be performed in Mimics (e.g. cut, move, reposition, resize). Mimics can import objects such as surgical guides, devices, and implants and position them as prepared for surgery. A user can then begin to analyze the placement of the imported implant/device. This helps both engineers designing the implant and surgeons placing the implant understand a designs fit and function as in figure 8.

Figure 8. 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 9 shows the anthropometric analysis tool and the ability to collect multiple data points and measurements for further manipulation and understanding.

Figure 9. 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 is a discrepancy in the demands of both engineers and clinicians for a 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 cranio-maxillofacial (CMF). Many tools within the software have been designed to fulfil 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.

1.1 Explanation To process data in Mimics, a set of stacked 2D cross-sectional images is first imported. These 2D images, commonly in the DICOM format, come from medical scanning equipment. Once the stacked images are imported, they can be viewed and edited using the various tools available in Mimics. The quality of the the 3D images that Mimics can create directly correlates to the slice thickness and pixel size of the 2D images. The Mimics screen is broken up into four main views; coronal, axial, sagittal, and 3D. Engineers can think of coronal as a front view, axial as a top down view, and sagittal as a right view. The axial view comes from the imported stack of images. To obtain the coronal and sagittal views, Mimics transposes the axial images into their respective positions. The 3D pane is where 3D models are visualized. Clicking on an image with the left mouse button automatically updates your location in all views.

Each of the 2D views contains a slice number in the lower right corner. The axial view also has a table position in the bottom left corner which describes the slices location in reference to the origin of the scanner table.

The main toolbar contains dropdown menus for most of the tools available in Mimics. Below the main toolbar is an icon list of frequently used tools.

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The project management toolbar is the database of all objects in Mimics. It contains tabs that correspond to each of the different object types such as masks, measurements, 3D objects, and curves. In the tabs, you will find the window where each object exists and all operations possible with that type of object. For example, under the 3D objects tab you can create new 3D models and delete existing models, among other things.

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1.2 Step by Step Tutorial Scenario: As a radiologist, you need to navigate through a patients scanned images and take certain measurements to aid in your diagnosis. The procedures outlined below will show you how to accomplish these tasks.

Navigation

Zooming and Panning

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 tool to make

this toolbar visible.

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 pulldown menu.

2. Turn on volume rendering

by clicking the Volume

Rendering button in the

3D toolbar.

3. Go through the pulldown 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.

Measurement Tools

Measurement Tools

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 Tools in the main toolbar.

2. Click once on one side of

the skull and again on the

other side, creating a

horizontal line.

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The measurement is displayed on the screen and in the Measurements tab. To hide the measurement simply click on the eyeglasses in the tab.

3. Scroll to axial slice 69.5. In the Measurements tab select New , then Measure Angle

.

4. Measure an approximate

angle of the jaw by clicking

once to start the

measurement, click again to

select where the angles

vertex is, and click once more

to end the measurement.

To change the location of the endpoints or vertex of the angle, drag the crosshairs.

Measure Density and Making Annotations

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 Tools 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 .

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3. Select the Annotations tab and click New .

4. Next click the image near the

elliptical measurement; this is

where the annotation will be

placed. Type sinus cavity in

the Text: section and click

OK.

The annotations text can be moved by left clicking on the text and dragging.

5. Save the file as Lesson1_your name.

1.3 Homework On the skull dataset from above, find the following measurements: the vertical distance from the top of the skull to the bottom of the skull, the angle between the spine and the bottom of the jaw, the density of the skull. You will need to decide which views to use for each measurement.

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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.

2.1 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 datapoints grayvalue, 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.

2.2 Step by Step Tutorial

Scenario: Your boss has asked you to review some scans and put together a presentation displaying a patients anatomy. You will use Mimics to highlight the bone structure of the hip, show where the aorta lies in relation to the hip, and create a 3D model to fully display the patients anatomy. The procedures outlined below will show you how to accomplish these tasks. In this section, you will use two different methods to create a mask displaying the hip. Then you will calculate 3D models of both masks.

Thresholding Toolbar

Thresholding classifies all pixels within a certain Hounsfield range as the same color, or mask. There

are predefined settings for certain biological materials available in the thresholding toolbar. A lower

threshold allows segmentation of soft tissue, whereas a higher threshold segments bone.

1. Open the hip_se.mcs project.

2. Select Thresholding in the main toolbar under segmentation.

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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.

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

Tools in the main toolbar. The cursor

will turn into a pencil.

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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.

5. 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.

6. Click Start thresholding in the

Profile Lines dialog box.

7. Hit Apply in the thresholding

dialog box since we are

keeping the 226 and 1634

threshold values. Click Close

in the Profile Lines box.

8. 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.

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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.

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.

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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.

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 your mask contains multiple objects and unless you want this, you should redo 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 .

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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

Aortas glasses

under Visible in

the 3D Objects

tab. This hides

and unhides the

3D model.

3. In the same tab,

click on the eye

glasses in the

Contour Visible

column and the

Visible column for

Bone-threshold.

When a 3D model is visible, clicking the contour visible eyeglasses will highlight the contours of the 3D object in the 2D views.

4. Now click the eye glasses under the

Triangle Visible column.

This option allows you to view the triangulated surface mesh of the object. For better visualization of the triangles, zoom in on the 3D image (hold Ctrl and the right mouse button while moving the mouse vertically).

5. Click the same eye glasses to turn the triangle visibility off.

6. Select Toggle Transparency in the 3D toolbar. You are able to view the internal shape of

the 3D object. Click Toggle Transparency again to return to normal.

7. Select Enable/disable clipping also in the 3D toolbar.

Clipping slices the 3D model according to the view you select, displaying the objects cross-section.

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8. In the

Clipping tab

make sure

the box under

Active is

checked next

to Axial.

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

10. To clip according to another viewing plane, simply select that view under Active (example

sagittal or coronal). You can also change the texturing of the cross-section by clicking on

Texture and changing it from object to slice to none.

11. Save the file as Lesson2_your name.

Capture Movie

Movies can be tailored to highlight different features depending on the application.

1. Click Capture Movie under Export in the main toolbar.

Under View to capture you can select which portion of the application you want to be included in the movie. Options range from the whole screen to just selected views. Note the output directory. You can change this to output to whatever file you want.

2. Select Bottom Right View for View to capture so that only the view containing the 3D model

will be included in the movie.

3. Hit the Record button to start the movie. Rotate the image around, zoom in and out, and

pan the image as you choose.

4. Click Stop when you are finished creating your movie. The movie will automatically open

in the software you have set up on your computer to view digital media.

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2.3 Homework On the skull_se.mcs dataset perform the appropriate thresholding and region growing to segment the soft tissue, bone, and mandible separately. Calculate 3D models. *You may need to readjust your threshold values so that the scanner equipment supporting the patients head is not included in the masks. Turn on transparency and create a movie of your choice including the models you created.

31


/ Mimics Lesson 3: Advanced Segmentation Tools to learn: Morphology Operations, Boolean Operations, Multiple Slice Edit, Edit Mask in 3D, measurement tools.

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


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

Advanced Segmentation First, separate the spine from the aorta using segmentation tools.

Multiple Slice Edit

Multiple Slice Edit is a timesaving tool because it allows you to apply the manual editing done on one

slice to other slices.

1. Open the heart_se.mcs project.

2. Create a threshold using the predefined Bone (CT) setting.

A bone threshold works well for this dataset because a contrast agent has been added so that the blood, or lumen, appears brighter and images similar to bone. This provides for better visualization in the CT.

3. Do a region grow to get

rid of floating pixels by

clicking on the mask in

some part of the spine.

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4. Select the yellow mask and click Duplicate Mask 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

The s key Switches to select

The d key Switches to deselect

9. 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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10. 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.

11. 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.

12. 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 taker longer to compute and are larger files. For more information about 3D settings see the help files.

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 above 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.

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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: , Number of pixels: 1, and

8-connectivity. Click Apply.

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: , Number of pixels: 1, and 8-

connectivity. Click Apply and name the resulting mask Morphology2_Aorta.

39


7. The erode broke any connections between the aorta and spine. This allowed just the aorta to be

selected after a region grow. However, now the mask is one pixel smaller so dilate must be used

to return the aorta to its original size.

8. Calculate a 3D model on high

quality.

9. If you notice spikes on the aorta resulting from the patients stent, use Edit Mask in 3D to get rid

of the protrusions and then recalculate the 3D model.

Boolean Operations

Boolean operations allow different combinations of two masks. We will use this tool to simulate the

wall thickness of the aorta.

1. Perform a Dilate of 3 pixels on the Morphology2_Aorta mask. Name the 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:

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.

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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.

3. Click on the top of the aorta and then

the bottom to get a distance along its

surface.

4. Now click Measure Distance under Tools 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.

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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.

3.3 Homework Re-open the heart_se.mcs dataset. 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 the lungs and how you would threshold for this. Next, create separate masks for the aorta and spine using Boolean operations. Also segment the heart. Your final result should be a 3D model of the heart, lungs, spine, and aorta.

42


/ Mimics Lesson 4: Surgical Simulation Tools to learn: Cut, Split, position an implant, import STL.

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


Scenario: You are a maxillofacial surgeon presented with a patient who has a diseased portion of the jaw and requires an implant. Use Mimics to prepare for your surgery by determining the cuts you will make to remove the diseased portion of the jaw and where you will position the needed implant. The procedures outlined below will show you how to accomplish these tasks. Surgical Simulation

Cut

Cutting can be done in either 2D or 3D. You have the ability to change the orientation and size of the cutting plane.

1. Open the skull_se.mcs project.

2. Click on Thresholding and select the

predefined Bone (CT) setting.

3. Select Region Grow and then click on the

mandible in the sagittal view. Name the

mask Mandible.

4. Create a 3D model using high quality.

5. Click on Cut with Polyplane under Simulation in the main toolbar.

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6. To make a cut, click once

behind the last molar and

double click your second point

at the base of the mandible.

You can change the orientation of the cutting plane by dragging the red arrowhead. If you cannot see the red arrowhead, left click on the plane and the arrow will reappear. The plane itself can be moved by dragging the green points located on each end of the cutting plane. Adjust the points as needed to make the cut as vertical as possible.

7. Select Properties in the

Cut with Polyplane

dialog box. Rotate the

model and change the

depth as well as any

other dimensions

needed to make the cut

go all the way through

the jaw (these

dimensions will vary

depending on where you

place your plane).

In the cutting plane properties dialog box you can change the depth, thickness, and extensions at the front and end of the cutting path. There is also a preview option to visualize how the plane will look with the specified dimensions.

8. Click Preview to view where the plane will cut and if everything looks okay, click OK to apply. If

the plane is not cutting where you want, readjust its dimensions.

44


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.

45


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.

46


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.

4.3 Homework On the femur_se.mcs project, make a cut that goes through the femoral head. Split the cut and position the femur_implant STL.

47


/ Mimics Lesson 5: CAD link Tools to learn: Polylines, IGES surfaces and curves, export to CAD.

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


Scenario: As an engineer you need to design a standard implant for a partial knee replacement. Before any design work can be done, the data from the CT scans must be imported into CAD. Use Mimics to create an IGES surface, which can be exported to CAD, to relay all the information necessary to begin the implant design. Follow the procedures in the step by step section to learn how to perform these steps.

Iges Surfaces

Export to CAD requires an Iges file. Mimics creates an STL surface mesh, but traditional CAD packages require a parametric surface file such as IGES. The MedCAD module allows us to create IGES surfaces and curves based on the anatomical geometry from the scan.

1. Open up the knee_se.mcs

dataset.

2. Create a mask on the knees

using lower and upper threshold

values of 120 and 3071.

3. Crop the mask so it only contains

the lower portion of the patients

left knee.

4. Select region grow and click

somewhere on this mask. Name

the new mask knee-1.

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5. Calculate a 3D model of knee-

1on 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: 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.

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.

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11. Go to Edit Masks and select Draw.

12. Draw in a connection where there is

a break in the mask.

13. Scroll up through the slices

continuing to fill in any breaks.

(Breaks occur on slices 60,75, 78,

84, 87, 90, 93, 96, 99)

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: . Rename this mask knee-3.

50


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 Control+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.

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 bottom portion of the knee (tibia), we can use editing to erase the knee cap and the remaining portion of the femur.

17. Delete the kneecap, which can be

seen in axial slices 39 through 93,

using the green up 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.

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18. Use Erase of Edit Masks to erase

the extra area of bone above the

tibia on axial slices 99, 102, and any

other slices above 102 that you may

have included when you cropped the

mask.

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 above

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 percentages limits (within 97% similar), the polylines are automatically added to the current polyline selection. A polyline selection is a portion of a polyline set.

22. Start at axial slice 0 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.

52


23. Scroll upwards until you get to a

slice where you need to reselect

which polyline you want to grow

(slice 48). Continue reselecting, as

needed, up through axial slice 96

(you will need to reselect on at

least slices 51, 57, and 60 and

maybe more).

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 96, select Update Polylines under Segme

Mimics Student Edition Course Book

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