Mimics Student Edition Course Book

SEMimics Student Edition Course Book 1 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 1.2 Explanation..............................................................................................................10 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 Explanation ............................................................................................................18 Step by Step Tutorial..............................................................................................18 / Mimics Lesson 2: Basic Segmentation .............................................................. 18 2.1 2.2 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 Need Help? Check out the Mimics User Community: http://uc.materialise.com/mimics 2 3.1 3.2 Explanation ............................................................................................................31 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 Explanation ............................................................................................................42 Step by Step Tutorial ..............................................................................................42 / Mimics Lesson 4: Surgical Simulation ............................................................... 42 4.1 4.2 Scenario: ......................................................................................................................................... 42 Cut .................................................................................................................................................. 42 Import and Reposition an STL ........................................................................................................ 45 4.3 Homework ..............................................................................................................46 Explanation ............................................................................................................47 Step by Step Tutorial..............................................................................................47 / Mimics Lesson 5: CAD link.................................................................................. 47 5.1 5.2 Scenario: ......................................................................................................................................... 47 Iges Surfaces .................................................................................................................................. 47 Export to CAD ................................................................................................................................. 54 5.3 Homework ..............................................................................................................55 Explanation ............................................................................................................56 Step by Step Tutorial ..............................................................................................56 / Mimics Lesson 6: Centerline creation ................................................................ 56 6.1 6.2 Scenario: ......................................................................................................................................... 56 Calculate and Export Centerline ..................................................................................................... 56 Cut Centerline Ending..................................................................................................................... 59 Modify Centerline ............................................................................................................................ 60 6.3 Homework ..............................................................................................................61 Explanation ............................................................................................................62 Step by Step Tutorial ..............................................................................................64 / Mimics Lesson 7: FEA (part 1) ............................................................................ 62 7.1 7.2 Scenario: ......................................................................................................................................... 64 Remeshing ...................................................................................................................................... 64 Material Assignment ....................................................................................................................... 67 Export to FEA ................................................................................................................................. 70 7.3 Homework ..............................................................................................................71 Explanation ............................................................................................................72 Step by Step Tutorial ..............................................................................................72 / Mimics Lesson 8: FEA (part 2) ............................................................................ 72 8.1 8.2 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 Need Help? Check out the Mimics User Community: http://uc.materialise.com/mimics industrial. using RP technology. STL file explanation An STL file is a triangulated surface mesh file. Accurate segmentation is important in order to extract meaningful information from images. typical CAD operations on a STL file instead of the traditional CAD files). During segmentation the user indicates the structure(s) of interest in the sliced image data. The software allowed extracting 3D information from an image stack and building a 3D model from it. The key to converting anatomical data from images to 3D models is a process called segmentation. The file contains the three nodes of each triangle and defines the normal direction of the triangle. This is necessary. Materialise offers an array of software solutions. SimPlant is Materialise’s dental implant planning software. it began as a rapid prototyping service bureau. Materialise ensures that all software packages are ISO-9001 certified and that there is a seamless link between all packages. This file format is ideal for anatomical geometry because of its Need Help? Check out the Mimics User Community: http://uc. The company also enjoys a worldwide reputation as provider of innovative software solutions. in RP. which can then be directly linked to rapid prototyping. since anatomical data is in general very intricate. plan out the surgery. 3matic is Materialise’s forward engineering software that allows advanced manipulation and design on an STL file. Materialise has grown into the world’s largest rapid prototype producer. This enables a more comprehensive 3D feel of the 2D data. Mimics uses 2D cross-sectional medical images such as from computed tomography (CT) and magnetic resonance imaging (MRI) to construct 3D models.materialise. Since then. create 3D models.e. In 1992 Materialise wrote software that linked the image information to RP models. Similar to SurgiCase. and linking the models to rapid prototyping (RP). For the medical and rapid prototyping industries. SurgiCase CMF is Materialise’s CT based craniomaxillofacial surgical planning software. surgical simulation and advanced engineering analysis. Mimics history After the start of the company Materialise in 1990 as a rapid prototyping company. and this usually consists of images in the XY plane (axial images). which is the common file format in RP. 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. Mimics uses the STL format.3 / Introduction Mimics (Materialise's Interactive Medical Image Control System) is Materialise’s software for processing medical images and creating 3D models. whereas a CT scanner does the reverse. From image to model A stack of images can be loaded into the software. Materialise’s Interactive Medical Image Control System (MIMICS) was born. best known for its activities in the field of rapid. and medical prototyping. It allows users to import patient data. computer aided engineering (CAE). Mimics. This information is then used to recreate a 3D model from the segmented structures. To describe the outer surface of the 3D model. / Overview Materialise Overview Materialise is an international company. and rapid prototype surgical guides that can be used during the operation to match the surgical plan. All medical software packages developed by Materialise are FDA approved. a 3D model is built slice per slice. Mimics then calculates and creates images in the XZ (coronal) and YZ (sagittal) direction. Magics RP is considered a powerful preprocessor for additive fabrication. The STL format allows describing the most complex geometries accurately. it allows users to plan dental implant surgeries and prepare surgical guides for the operating room. CAD. it breaks down a 3D model (the human body) into a stack of image slices. and fix and remesh for CAE. Mimics is the medical image based processing tool for creating 3D models. Started in 1990 as a spin off corporation from the University of Leuven in Belgium. and surgery planning. computer aided design (CAD). It allows a user to perform ‘digital’ CAD operations (i. It prepares 3D object (STL) files for additive fabrication as well as performs easy mesh and geometry manipulation. it didn’t take long for the company to see the analogy between RP and CT (or MRI) images. As such.com/mimics . Mimics allows the user to create models based on the grayvalues (Hounsfield units in CT images) within these images. This makes editing very easy. Need Help? Check out the Mimics User Community: http://uc. Mimics has the flexibility to create models from any geometry distinguishable within the scanned data. and models created. since it allows true editing in 3D. The accuracy in a Mimics model matches the accuracy of an object captured within the scan. A grayvalue is a number associated with an image pixel defining the shade (white. Figure 1. Segmentation The medical images coming from CT or MRI scanners consist of grayscale information. but Mimics also has a unique 3D editing tool.4 simple file structure and flexibility to match any contour desired. This type of segmentation is called thresholding and yields accurate models. which is easier to comprehend than 2D editing. Mimics can calculate a 3D model (Figure 2). Below is an example of the triangulation of an STL file. the image data can be segmented. It is not controlled by parametric constraints such as true CAD files and IGES files.materialise. gray. Using the segmentation and known information on the pixel size and the distance between the image slices. XZ or YZ). Many of the segmentation tools in Mimics are common in image processing and can be applied in any of the views (XY. Because of this. By grouping together similar grayvalues. Editing a Mimics model in 3D to capture only the femoral head.com/mimics . an initial segmentation can be optimized in a 3D preview (Figure 1). There is a direct association between material density of the scanned object and the grayvalue assigned to each pixel in the image data. or black) of the pixel. 5 Figure 2. Continuous developments and the inclusion of new tools continue to widen the application base. Mimics development continuously strives to optimize this “pre -processing” to ensure a fluent workflow from images to application. Mimics models printed on a RP machine with support generation. Figure 3. RP The 3D object created within Mimics is an STL file. holding a physical model is always easier to understand than a 3D model on a computer screen. no matter how good 3D graphics are. The applications of Mimics Although Mimics was originally designed to link medical images to rapid prototyping. Considering the fact that the human brain is optimized to work with something tangible. Or it can be imported into Materialise’s Magics program for support generation or for build optimization. Rapid prototypes from Mimics have many applications in the medical field. in the latter it also allows support generation.materialise. Need Help? Check out the Mimics User Community: http://uc. there are of course many applications possible using the 3D model that is calculated after segmentation. 3D objects calculated from CT images.com/mimics . 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. STL is the common language for rapid prototyping machines and 3D printers and it can describe very complex geometries (like medical geometries). 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. The 3D object can be directly exported to rapid prototyping in either STL or Sliced file format. Over the years Mimics evolved to “the Golden Standard” in linking medical images to various applications. but for CAE it is. the models are helpful in communication and surgery preparation for clinical work. function. Hence. Analyses such as finite element analysis (FEA). For analyzing bridges or buildings this is understandable. 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.materialise.6 Since the models accurately match patient data. In the early days of CAE.com/mimics . Medical rapid prototypes are highly utilized by medical device design manufactures and engineers. The difference between an STL file of an abdominal aortic aneurysm prepared for rapid prototyping (left) and FEA (right). and kinematics allow researchers and engineers to put actual patient data to the test without the inconvenience of physical testing. the shape of the triangles is not important. Therefore for accurate analysis. fit. Since STL also uses small elements (triangles) to describe a 3D model. Figure 4 shows the difference between an STL file prepared for RP compared to CAE. The magnitude of the variable is usually visualized with colormaps. In order to do so. people used CAD designs as a starting point for their geometrical input. stored in STL format. The RP models allow engineers to test form. since the stress in one end of the triangle can be significantly different from the stress in the other end. the number of triangles in a mesh must be reduced. CAE softwares require STL files that use equilateral triangles to describe the 3D. Also to reduce the computation time in CAE software. but complex anatomical data is impossible to design in a CAD package. discrete elements and calculates the variables for every element. computational fluid dynamics (CFD). CAE software divides the model in tiny. The complete process of triangle shape optimization and triangle reduction is called remeshing. For RP however. CAE Advancements in computer aided engineering (CAE) have provided engineers with the ability to test designs prior to ever building a physical model. Need Help? Check out the Mimics User Community: http://uc. a force is applied to a certain anatomical part and CAE software then calculates the resulting stresses and strains. Starting from image information ensures accurate geometry. very sharp elongated triangles are not suitable for analysis. the link with this application is obvious. Mimics can optimize the shapes of the triangles before exporting them for CAE analysis. Figure 4. this reduces the number of elements and nodes the analysis programs have to calculate. In FEA for example. Material properties Most CAE programs allow the user to assign constant material properties for individual objects.). To do an analysis. This volume mesh generation flexibility allows a user to determine what parameters and settings are most important depending on application and preference. Need Help? Check out the Mimics User Community: http://uc. This information is used in Mimics to accurately assign material properties to the elements of the volume mesh (Figure 7). Anatomical structures. Mimics will create this node-to-node matching from two seperate STL files as shown in figures 5. Volume Mesh STL is a surface representation. a complete volume description is needed. In the greyscale images from the CT scan there is more information than just the geometrical shape of an anatomical part. and 6. This will quickly prepare anatomical models for CAE analyses. By utilizing Mimics’ remeshing tools. While running a finite element analysis of an assembly it is important for two mating surfaces to have node-to-node matching. Mimics can automatically perform the remeshing processes described in the above section. such as bone. Mimics has the option to perform manual remeshing. with optimized mesh and node-to node matching. Figure 6.com/mimics . Generating a volume mesh from an optimized surface mesh is straightforward. For highly sensitive analyses and for more user control and definition. This allows a user to manually edit triangles and control the triangle reduction and size.materialise. Two parts. Mimics will analyse the shape quality of each triangle. As described in the section about segmentation. Original mesh of two surfaces without node-to-node matching. To optimize the mesh and create equilateral triangles.7 Remeshing Mimics has been designed to remesh 3D objects (STL files) from their original RP-ready format to a CAEready format. Figure 5. From a triangle surface mesh a tetrahedral volume mesh can be generated. flow. A tetrahedral and hexahedral mesh can be created within rd Mimics or within a 3 party volume mesh generation package. The remeshing process in Mimics also allows one to analyse an anatomical assembly. have varying material properties throughout the structure. 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. the grayvalues represent material density. etc. a user can observe actual anatomical data reacting under applied constraints (loads. After the quality of each triangle within a mesh is understood. heat. the softer trabecular bone is blue/green. verification. the surface needs to be mathematically described (NURBS). Surgical simulation of the placement of a femoral implant. Mimics has provided a link to take patient data directly to the 3D CAD platform for design. Need Help? Check out the Mimics User Community: http://uc. Typical OR procedures can also be performed in Mimics (e. resize). move. cut. it is best to keep working on STL level. This helps both engineers designing the implant and surgeons placing the implant understand a design’s fit and function as in figure 8. it allows design changes directly on the STL. whereas the denser cortical bone is orange/red. A user can then begin to analyze the placement of the imported implant/device. Mimics can import objects such as surgical guides. The Mimics CAD link allows users to create IGES curves and surfaces from anatomical surfaces and import them into any CAD software. Also here.5. This process of reverse engineering is quite tedious and time-consuming and leads to a simplification of the surface. devices.8 Figure 7. Surgical Simulation Mimics helps bridge the gap between clinicians and engineers. a surgery can be performed within the virtual world prior to entering an operating room (OR). To be able to design accurate implants. 3-matic (by Materialise) fills a need. Figure 8.com/mimics . With Mimics’ surgical simulation functions. CAD For engineers designing equipment such as medical implants and devices.materialise. reposition. Colored visualization of the material properties of the different elements in a section of a femur. For true CAD applications.g. and implants and position them as prepared for surgery.1. and sizing studies. Distributed material property assignment for an FEA analysis based on the grayvalues in a CT scan. 3-matic is described in more detail in chapter 3. As is clear from this chapter. Because Mimics is used in multiple markets. Before You Start Install Libraries Make sure to install the Anthropometry and Distractor libraries which can be found on the Mimics SE CD.com/mimics . whereas clinicians want it to be easy to use and fast. E. Mimics provides a link to many applications. Mimics can also calculate a reconstructed X-ray from the image information. Anthropometric Analysis and the visualization of the analysis points on a reconstructed X-ray. Phrases in bold represent tools in Mimics. Mimics is an easy to use. Therefore. but also clinicians. highly effective research tool. This opened up possibilities in many markets.   Anything in italics and double quotation marks represents what you should type. Engineers want a powerful open toolbox. technical/industrial design. Therefore Mimics has a modular structure and users can tune the software to their needs by extending the basic package with additional modules. Mimics is equipped with a very user friendly graphical user interface (GUI) as well as powerful tools to analyze intricate data. With the ability to create unique measurement studies that can be applied to multiple datasets. Need Help? Check out the Mimics User Community: http://uc. This user feedback is invaluable for the development of the software and to create a well rounded. 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. Figure 9. The major industries that use Mimics are Orthopaedic. Users of Mimics often identify tools that would make their research and work more efficient. it is important for the software to have features that fit each market. Figure 9 shows the anthropometric analysis tool and the ability to collect multiple data points and measurements for further manipulation and understanding. Discussion and Conclusion Mimics is a powerful image processing tool and links to many applications. powerful toolbox for both engineers and clinicians.materialise.9 A user can use Mimics to study anatomy and create measurement studies to analyze and classify data. Many tools within the software have been designed to fulfil needs and requests of these markets. Of course Mimics provides a seamless link with other Materialise software. anthropology. the same measurements can be acquired from various patients to aid research. There is a discrepancy in the demands of both engineers and clinicians for a software like Mimics.g. and pulmonary study. Other industries Mimics is also used in include tissue engineering. Its user base consists mostly of engineers. and craniomaxillofacial (CMF). 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. This is very convenient for clinicians who are used to ‘reading’ X-ray images. Magics for RP applications and 3-matic for CAE or design (CAD). Cardiovascular. To accommodate the wishes of both. To obtain the coronal and sagittal views. These 2D images. they can be viewed and edited using the various tools available in Mimics.materialise.1 Lesson 1: Mimics Navigation Explanation Tools to learn: Navigation. Each of the 2D views contains a slice number in the lower right corner. a set of stacked 2D cross-sectional images is first imported. commonly in the DICOM format. and 3D. axial as a top down view. project management. Need Help? Check out the Mimics User Community: http://uc. Engineers can think of coronal as a front view. Mimics transposes the axial images into their respective positions. Once the stacked images are imported. Clicking on an image with the left mouse button automatically updates your location in all views. and sagittal as a right view. The 3D pane is where 3D models are visualized. 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 main toolbar contains dropdown menus for most of the tools available in Mimics. coronal. To process data in Mimics. axial. The Mimics screen is broken up into four main views.com/mimics . come from medical scanning equipment.10 / 1. Below the main toolbar is an icon list of frequently used tools. The axial view comes from the imported stack of images. The axial view 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. basic measurement tools. sagittal. For example. you will find the window where each object exists and all operations possible with that type of object.com/mimics . 3D objects.materialise. and curves.11 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. Need Help? Check out the Mimics User Community: http://uc. under the ‘3D objects’ tab you can create new 3D models and delete existing models. amon g other things. In the tabs. Arrow Up/ Page Up Rotate up with discrete steps. Panning moves an image up. Click on Unzoom and then the view you want to restore to return the image to its original location. Select Pan Once in the main toolbar. Navigation Zooming and Panning Zoom allows you to view a close-up of a selected region. Arrow Right / End Rotate right with discrete steps.12 1. and coronal views. like the tools learned in the Zooming and Panning exercise. The procedures outlined below will show you how to accomplish these tasks. Arrow Down / Page Down Rotate down with discrete steps. 2. select Zoom to Full Screen and click anywhere on the images. 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. Need Help? Check out the Mimics User Community: http://uc.2 Step by Step Tutorial Scenario: As a radiologist. Click on the Zoom tool in the main toolbar. Left click and drag on a view to pan an image.com/mimics . This only works when the mouse is in the 3D pane. you need to navigate through a patient’s scanned images and take certain measurements to aid in your diagnosis. CTRL + Right mouse button Zoom: Move the mouse vertically while keeping the buttons pressed to zoom in and out. 1. To restore the images’ size click on Zoom to Full Screen again. Arrow Left / Home Rotate left with discrete steps. Shortcuts Key combinations can be used in place of certain tools. This only works in the axial. Select the Unzoom tool and click on the same image you just zoomed in on. To create a full screen view. 6. 5. SHIFT + Right mouse button Pan: Move the mouse while keeping the buttons pressed. left or right. These shortcuts can help optimize image processing and workflow. 4. sagittal. Change contrast of 2D views: Move the mouse while holding the right mouse button down. down. Drag a box around the axial view of the image by holding down the left mouse button. 3.materialise. Click on ‘Help’ in the main toolbar then ‘General Help’ to access the help files.materialise. information on importing images can be found in the help files under the ‘Contents’ tab by selecting ‘Mimics Tutorial’ and then ‘Import’. to make Each tab of the project management toolbar represents a type of object in Mimics. Click through the tools of the different tabs to familiarize yourself with what is available. Need Help? Check out the Mimics User Community: http://uc. the full list of tools can be seen by clicking on the Actions button . 2. 3. Click on the Context Help icon in the main toolbar and then click on any tool to view its help file.com/mimics . Click the red ‘X’ to close the help files. The most frequently used tools for each tab are located along the bottom of the tab. 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. 1. However. however. 2. All of the objects for a project are shown here.13 Help Pages The help pages contain in-depth information about tools and tabs. Select the Project Management tool this toolbar visible. Note – The step of importing images is not explained in this tutorial since Mimics Student Edition does not allow importing. com/mimics . Need Help? Check out the Mimics User Community: http://uc. 1. The histogram pictured shows the window of pixels mapped in the image. To map this scale onto the 256 gray values of your computer. and even bone can be emphasized depending on the window chosen. Select different contrasts in the drop down menu.14 Windowing The gray values of CT images are expressed according to the Hounsfield scale shown below.materialise. 2. Mimics has a feature called windowing. Windowing is a tool to adjust the image contrast. muscle. Differences between fat. soft tissue. The shortcut for changing the contrast of an image is to right click on an image and drag the mouse. Notice how different scales allow better visualization of certain tissues. which has 4096 values. Change the contrast of the images by moving the line or the endpoints on the graph located in the ‘Contrast’ tab of project management. 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.15 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. Measure Distance and Measure Angle calculate data from either the 2D scans or 3D model. creating a horizontal line. 2. Turn on volume rendering by clicking the Volume Rendering button 3D toolbar. Go through the pulldown menu selecting the different predefined settings to see all of the visualization options.5 and click Measure Distance 2. Turn off volume rendering by clicking the Volume Rendering button again. Scroll to axial slice 180. 4. 1. Volume rendering can consume a lot of system resources slowing down computer processing time. but gives a nice impression of what your model will look like. It is only a visualization tool. so remember to turn it off when you are done. Need Help? Check out the Mimics User Community: http://uc. Measurement Tools Measurement Tools Different tools are available to collect information from scanned images.com/mimics . Click once on one side of the skull and again on the other side.materialise. in the 3. under ‘Tools’ in the main toolbar. Any of these measurements can then be exported to text for further analysis in statistical packages. and the standard deviation of a selected region. In the ‘Measurements’ tab select New . measurement simply click on the eyeglasses in the tab. and click once more to end the measurement.16 The measurement is displayed on the screen and in the ‘Measurements’ tab. Select Measure Density in Ellipse from ‘Tools’ and select the circular area of the sinus cavity. drag the crosshairs. mean hounsfield unit. Measure an approximate angle of the jaw by clicking once to start the measurement. 4.com/mimics . As you scroll through the image. 3. and standard deviation from the mean. Notice that this tool gives you the area of the ellipse. 2. Scroll to axial slice 113.Measure Density in Rectangle . The same type of tool is also available in a rectangular shape . 1. Annotations can be used to point out measurements or structures in the images. You can change the size of the density tool by grabbing the handles.5.materialise. Measure Density and Making Annotations Measure Density measures the area. click again to select where the angle’s vertex is. then Measure Angle To change the location of the endpoints or vertex of the angle.5. To hide the . Need Help? Check out the Mimics User Community: http://uc. mean value of the density. Scroll to axial slice 69. the location of the measurement will not change. the angle between the spine and the bottom of the jaw. the density of the skull. . 5. Select the ‘Annotations’ tab and click New 4. Type “sinus cavity” in the ‘Text:’ section and click ‘OK’.com/mimics .materialise. The annotation’s text can be moved by left clicking on the text and dragging. this is where the annotation will be placed. 1.3 Homework On the skull dataset from above. Next click the image near the elliptical measurement. find the following measurements: the vertical distance from the top of the skull to the bottom of the skull. You will need to decide which views to use for each measurement. Save the file as “Lesson1_your name”. Need Help? Check out the Mimics User Community: http://uc.17 3. 2. 1. Edit Mask provides the tools needed to draw. Different options are available for the quality of 3D model created.materialise. automatically determining threshold values. 2. or mask. Instead. To perform the transformation from 2D into 3D. Region Growing allows just this and is also useful for removing floating pixels. Thresholding is used to classify all pixels within a certain Hounsfield range as the same color. and create a 3D model to fully display the patient’s anatomy. Mimics has various exporting options including exporting in the STL format or even exporting movies. basic editing tools.1 Explanation The first step in creating a 3D image from 2D data is segmentation. There are predefined settings for certain biological materials available in the thresholding toolbar. Mimics has a selection of editing tools.2 Step by Step Tutorial Scenario: Your boss has asked you to review some scans and put together a presentation displaying a patient’s anatomy. Mimics creates a mask based off of how surrounding pixels compare to a selected datapoint’s grayvalue. or section. With Dynamic Region Growing thresholding does not need to be done first. The procedures outlined below will show you how to accomplish these tasks. regions of interest. The mask that is selected in the project management ‘Masks’ tab is considered the active mask. Need Help? Check out the Mimics User Community: http://uc. 3D calculation parameters can be set manually using the custom setting. This tool proves very useful for segmenting structures such as blood vessels and nerves. you will use two different methods to create a mask displaying the hip. Calculate 3D is used. For example. Calculate 3D. Region Growing. In this case. You will use Mimics to highlight the bone structure of the hip.18 / Mimics Lesson 2: Basic Segmentation Tools to learn: Thresholding. High quality can give a smoother. Thresholding Toolbar Thresholding classifies all pixels within a certain Hounsfield range as the same color. For more information on quality settings and parameters. or locally threshold a specific mask. Select Thresholding in the main toolbar under segmentation. 2. Crop Mask restricts segmentation to a designated area by removing everything from a mask that is outside a selected bounding box. or mask.com/mimics . By setting only a lower threshold value. If necessary. Dynamic Region Growing. Alternatively. more accurate model. Low and medium quality have short calculation times but may produce a more approximated model. Depending on the type of file output needed. A lower threshold allows segmentation of soft tissue. however the most accurate will be from using the optimal setting. see “Calculate 3D” in the help files. an upper and lower threshold value can be set. To further segment various parts of an image. whereas a higher threshold segments bone. a mask may need to be separated into numerous objects. Then you will calculate 3D models of both masks. Mimics has several tools to segment. the pixels falling within the designated range will make up a single mask. show where the aorta lies in relation to the hip. create movie. In this section. 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.mcs’ project. Different sections of an image can be highlighted using different masks. erase. Open the ‘hip_se. all pixels higher or equal to the set value will comprise the same mask. After thresholding. 5. Click through the predefined thresholds to view how different thresholds highlight different areas of the images. This tool displays how the gray value changes along a line within the image. Select the ‘Bone (CT)’ threshold and click ‘Apply’.com/mimics . Select Draw Profile Line under ‘Tools’ in the main toolbar. The cursor will turn into a pencil.materialise. as done in the previous exercise. A mask is visible when the eyeglasses under the ‘Visible’ column of the ‘Masks’ tab are showing. 4.19 3. You can manually set the threshold by changing the minimum and maximum values. 2. 1. Select New Mask . Any editing will be performed on the active mask. Scroll to axial slice 40. Rename the mask “BoneThreshold” by clicking ‘Green’ in the ‘Masks’ tab until you see a blinking cursor signifying the text can be changed. A mask is considered active when it is highlighted. Need Help? Check out the Mimics User Community: http://uc. Thresholding with Draw Profile Line Draw Profile Line is another way to threshold an image. Threshold values can also be changed in the ‘Thresholding’ dialog box. 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. click the Locate button . You will see horizontal lines to indicate these values. Clicking ‘Scale to Fit’ provides a zoomed in view of the peaks along the profile line. 7. Remember that thresholding must be done prior to region growing. 5. If you need to find where a profile line is located. 6.20 3. In this case a good threshold for bone is the predefined bone (CT) setting which is 226 to 1634. Click ‘Close’ in the ‘Profile Lines’ box. a rule of thumb for selecting bone on CT images is to put the lower threshold on 1/3 of the cortical peak. You want the profile line to cross over your region of interest and into surrounding regions. Need Help? Check out the Mimics User Community: http://uc. Leave the upper threshold at 1634 and the lower threshold at 226. Region Grow Region growing is used to separate masks into different parts as well as to get rid of floating pixels. 8. Click once below the femur to start the profile line and once above the femur to end the profile line. Lowering the threshold selects soft tissue and increasing the threshold selects dense cortical bone. You can move the upper and lower threshold values by clicking ‘Start thresholding’ in the ‘Profile Lines’ dialog box. Otherwise.materialise.com/mimics . Name the mask “Bone-Profile line”. Click ‘Start thresholding’ in the ‘Profile Lines’ dialog box. Hit ‘Apply’ in the thresholding dialog box since we are keeping the 226 and 1634 threshold values. You will see the profile line appear in the measurement tab of the project management toolbar. Keep ‘Multiple Layer’ checked so region growing will be done on the entire dataset instead of just one layer.materialise.com/mimics . Select ‘Source (= BoneThreshold)’ and ‘Target mask (= New Mask)’. The mouse will turn cross -shaped.21 1.Profile line”. from the ‘Segmentation’ toolbar. 4. 3. Click somewhere on the hip. all selected information will be removed from the target mask and placed in the source mask (compare it to cut and paste). You will notice that now the cyan mask only contains bone. 5. Rename this new mask “Bone2-Threshold”. If you uncheck ‘Leave Original Mask’. 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. Select ‘Close’ to get rid of the region growing toolbar. unlike the green mask which included other structures as well. Repeat the procedure for region growing on the ‘Bone-Profile line’ mask. Make sure ‘Leave Original Mask’ is checked. Need Help? Check out the Mimics User Community: http://uc. Select Region Growing 2. Name the new mask “Bone2. Make sure the ‘Bone2-Threshold’ mask is highlighted and select high quality. Most major tools have three locations. and as an icon in the main toolbar. 3. in their corresponding tab of project management. click ‘No’. click Toggle Reference Planes . If a message pops up saying the resulting 3D model will consist out of different parts. 4. Click ‘Calculate’. Click on the ‘Bone2threshold’ mask in the ‘Masks’ tab of the project management toolbar. This button can be found at the bottom of the mask tab. Custom parameters can be set for the 3D calculation. Clicking outside the center of the object will rotate around the axis perpendicular to the viewing angle.materialise. Select the Calculate 3D button . under their specific heading in the main toolbar. If you want to remove the toggle reference planes from the 3D pane. you should redo a region grow on the mask. Rotate the 3D model by holding the left mouse button in the 3D view and moving the mouse around.22 Calculate 3D Transform data from the 2D images into a 3D model. under segmentation in the main toolbar. or in the icon list on the main toolbar. 2.com/mimics . 1. Receiving such a message indicates your mask contains multiple objects and unless you want this. For more information on these settings look under ‘calculate 3D’ in the help files. Need Help? Check out the Mimics User Community: http://uc. Clicking near the center of the object will rotate around the vertical and horizontal axes. 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. Enter the following coordinates so that only the lower portion of the hip and spine are shown in the mask. 1. Need Help? Check out the Mimics User Community: http://uc. Select the ‘Bone2. Crop Mask With Crop Mask you can manually change the boundaries of your mask or enter the desired coordinates.com/mimics .Profile line’ mask using the same procedure as for the ‘Bone2-Threshold’ mask. You can also crop the mask by resizing the bounding box on the image. Click on Crop Mask under ‘Segmentation’.materialise.23 5. You will notice that both masks result in the same 3D model even though different thresholding methods were used to create them. 2.Threshold’ mask. Calculate a 3D model of the ‘Bone2. 3. Zoom in on axial slice 115. We will use such tools to separate the vertebral column from the pelvic bone. 3. (To achieve the same view as the pictures for step 4. Set the ‘Type:’ to circle. Now the mask will only be shown in the region that was outlined by the crop mask bounding box. the other masks’ visibility have been turned off) Edit Mask The area contained within a mask can be modified using the edit mask tools. Click ‘OK’. Click Edit Masks under ‘Segmentation’ and select ‘Erase’ in the Edit Masks toolbar.materialise.com/mimics . and set the ‘Width:’ to 20 (the height will automatically be changed to 20 also).24 4. check the ‘Same Width & Height’ box. Need Help? Check out the Mimics User Community: http://uc. 1. Make sure the ‘Bone2Threshold’ mask is active. 2. Scroll up through slice 175 continuing to erase the pelvic bone on each slice.com/mimics . 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.25 4.materialise. The erased region will turn from the original color of the mask to the original scan data. Need Help? Check out the Mimics User Community: http://uc. 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. 5. 26 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. Click on the Dynamic Region Growing tool . Check the ‘Multiple Layers’ and ‘Fill Cavities’ boxes. 2. Need Help? Check out the Mimics User Community: http://uc.materialise.com/mimics 27 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. Need Help? Check out the Mimics User Community: http://uc.materialise.com/mimics 28 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. Need Help? Check out the Mimics User Community: http://uc.materialise.com/mimics 29 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. Need Help? Check out the Mimics User Community: http://uc.materialise.com/mimics bone.30 2. Calculate 3D models. Turn on transparency and create a movie of your choice including the models you created.3 Homework On the ‘skull_se.mcs’ dataset perform the appropriate thresholding and region growing to segment the soft tissue.com/mimics . *You may need to readjust your threshold values so that the scanner equipment supporting the patient’s head is not inc luded in the masks. Need Help? Check out the Mimics User Community: http://uc. and mandible separately.materialise. appears brighter and images similar to bone. With this tool you can immediately see how the editing you do changes the 3D model. 3. 3. measurement tools. This provides for better visualization in the CT.1 Segmentation will always follow a procedure of threshold to select a region of interest. Morphology Operations becomes useful. Multiple Slice Edit. 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. 1. or lumen. Assume this patient has some type of stent supporting his or her aorta. Editing can even be done in the 3D view with Edit Mask in 3D. Boolean Operations. Do a region grow to get rid of floating pixels by clicking on the mask in some part of the spine. Multiple Slice Edit can be used to copy the editing done on a single slice onto other slices. Open the ‘heart_se. Advanced Segmentation – First.com/mimics . and edit mask to focus on an area of interest. The procedures outlined below will show you how to accomplish these tasks. A bone threshold works well for this dataset because a contrast agent has been added so that the blood. 3.31 / Mimics Lesson 3: Advanced Segmentation Explanation Tools to learn: Morphology Operations. 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. separate the spine from the aorta using segmentation tools.2 Step by Step Tutorial Scenario: As a researcher you want to explore the interaction between the heart and the aorta. Need Help? Check out the Mimics User Community: http://uc. and Boolean Operations that allow quicker and easier segmentation. However. You can use the tools in Mimics to break this connection and also find out more information relevant to your research. Mimics contains various advanced segmentation tools such as Multiple Slice Edit. however. The previous tutorial on segmentation gave you the basic tools needed to manipulate scanner data. Create a threshold using the predefined ‘Bone (CT)’ setting. Morphology Operations.mcs’ project. region grow to remove floating pixels. 2. When two elements need to be disconnected yet have a point of contact that is difficult to identify.materialise. This is useful especially for eliminating scatter or disconnecting two body parts that touch in more than one slice. before further analysis can occur the aorta’s connection with the spine must be broken. Edit Mask in 3D. Changes size of cursor Switches to select Switches to deselect 8. Select the yellow mask and click Duplicate Mask Rename the cyan mask ‘Spine’. Shortcuts for multiple slice edit: CTRL + left mouse button The ‘s’ key The ‘d’ key 9.32 4. Change ‘Copy to slices:’ to ‘Sagittal’ and make sure ‘Select’ is marked. or height.materialise. . 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’. Set the ‘Copy to slices’ to 1.26 in the sagittal view and highlight the region of the spine that borders the aorta (as shown in the picture). 7. 5. the mask is now copied to the next slice. We recommend keeping this number low so you can evaluate each selection as you scroll through the slices. in the project management ‘Mask’ tab. You can control the size and shape of your editing tool by changing type.com/mimics . Press the green up arrow. ‘Select’ adds pixels to a slice and deselect removes pixels. For this exercise a circle of width and height 20 works well. width. Under ‘Segmentation’ in the main toolbar click Multiple Slice Edit 6. Scroll to slice 114. Need Help? Check out the Mimics User Community: http://uc. 37.materialise.33 10. 129. The aorta should now show up in a mask of its own. separate from the spine. Need Help? Check out the Mimics User Community: http://uc. Be careful not to include the aorta in your highlighting. changing it as needed as the boundary of the aorta and spine moves. use ‘Select’. this means the aorta is still connected to the spine somewhere and you need to scroll back through the images to delete this connection. Rename this mask “Aorta” then calculate a 3D model on high quality.46. use ‘Deselect’ to erase.com/mimics . If you need to select more of the spine. Make sure to modify the mask. If it does not. The pictures show examples of slice 126. 11. Depending on how well you separated the aorta from the spine. Later in the tutorial you will learn how to edit these using Edit Mask in 3D. If some of the aorta is selected by accident. Click ‘Apply’ when done. Click the region grow tool and then click on the aorta (shown in pink). 12. and 130.39. Repeat the above step through all the sagittal slices up through slice 134.77. your 3D model might contain some small vessels branching off of the aorta. Click the interpolate tool The interpolation algorithm requires a selection in at least two slices with at least one empty slice in between. High and optimal quality models have better accuracy but taker longer to compute and are larger files. Change ‘Copy to slices:’ to ‘Sagittal’ and make sure ‘Select’ is marked.materialise. 2. This takes the place of doing manual editing on many slices.98 and highlight the spine again. the accuracy of the model is more approximated. Need Help? Check out the Mimics User Community: http://uc. Under ‘Segmentation’ in the main toolbar click Multiple Slice Edit 4. however. 1. . Click the glasses under ‘Visible’ to hide the 3D model created above. 5. 6.com/mimics . Rename We will accomplish the same task of separating the spine from the aorta using an alternate method. For more information about 3D settings see the help files. Interpolate Interpolate creates a temporary mask that extends between two selected slices. Scroll to slice 125.34 You can choose different quality settings for 3D model calculation. Create another duplicate of the yellow mask by selecting it and clicking Duplicate the new mask “Aorta-interpolate”. then click ‘Apply’. Highlight the spine on sagittal slice 113. 7. Low and medium quality create faster models that have smaller file sizes. .28 to break connections between the spine and aorta. 3. 9. Again.com/mimics . Need Help? Check out the Mimics User Community: http://uc.46 and the last slice as 132. The aorta is now separated from the spine with a few quick steps.35 8.32. Do a region grow on the aorta. Repeat the interpolate procedure with the first slice as 126.materialise. you may see some branching off of the aorta depending on your previous editing. rename the mask “Aorta2” and then calculate a high quality 3D model. 3. Click the Region Grow tool and select the heart. Increase the bounding box in the 2D views to include more of the vessels. Select Edit Mask in 3D under ‘Segmentation’ of the main toolbar. 2. Set the lower threshold value to 270 then click ‘Apply’. Need Help? Check out the Mimics User Community: http://uc. 6. In the 3D model you can see the vasculature branching off of the heart. You will use this tool to remove some of the small vessels coming off of the heart.36 Edit Mask in 3D Editing can be done on a mask in the 3D view. 1. Calculate a 3D model on high quality. Click the New button in the project management ‘Mask’ tab.materialise. 4. 5. Name the resulting mask “Heart”.com/mimics . however a new 3D model must be calculated after editing is done in order to view the changes. 9. Rotate the model to access all of the vessels. Calculate a 3D model of the new mask on medium quality and notice how the vessels you deleted are gone. Click ‘Remove’ and the vessels disappear from the 3D view. Once an area is selected it turns a different color. Need Help? Check out the Mimics User Community: http://uc. 8. Make sure ‘Select’ is picked in the Edit Mask in 3D dialog box. 11. In one of the 2D views. Highlight the majority of small vessels branching off of the heart.materialise. 10. Save the project as “Heart_your name”.com/mimics . do a region grow on the ‘Heart’ mask you modified in the above steps.37 7. Change the color of the ‘Erode_Aorta’ mask to light blue so you can see the effect of performing an erode. You can use a morphology operation as an alternative to multiple slice edit for separating the aorta from the spine. 6. ‘Number of pixels: 1’. ‘Number of pixels: 1’. Close performs a dilate followed by an open. Create a duplicate of the ‘Aorta’ mask. Select Erode with ‘Source: Morphology_Aorta’. Need Help? Check out the Mimics User Community: http://uc. Select Dilate with ‘Source: Erode_Aorta’. Click ‘Apply’. Name the mask “Morphology_Aorta”. useful for filling cavities within a mask. Click ‘Apply’ and name the resulting mask “Morphology2_Aorta”.38 Morphology Operations Morphology operations take or add pixels to the source mask. This is useful for breaking small connections. and ‘8-connectivity’. 3. Click Morphology Operations under ‘Segmentation’ in the main toolbar. Open performs an erode followed by a dilate. 2.com/mimics .materialise. and 8 connectivity. 8-connectivity considers only pixels in the surrounding plane whereas 26-connectivity looks at neighboring pixels in 3D. Do a region grow on the aorta and name the resulting mask ‘Erode_Aorta’. 5.‘Target: <New Mask>’. Erode takes away the number of pixels selected and dilate adds the number of pixels to the boundary of the mask.‘Target: <New Mask>’. 1. 4. We will use this tool to simulate the wall thickness of the aorta. ‘Operation: Minus’. Other Boolean operations include finding the intersection and the union of two masks. This allowed just the aorta to be selected after a region grow. Make sure ‘Mask A: Bool’. 8. Perform a Dilate of 3 pixels on the ‘Morphology2_Aorta’ mask. Boolean Operations Boolean operations allow different combinations of two masks. ‘Mask B: Morphology2_Aorta’ and ‘Result: <New Mask>’ are all selected. 1. 2. 9.com/mimics . Need Help? Check out the Mimics User Community: http://uc. now the mask is one pixel smaller so dilate must be used to return the aorta to its original size. Name the mask “Bool”. Click ‘Apply’. Select Boolean Operations from ‘Segmentation’ in the main toolbar.materialise. If you notice spikes on the aorta resulting from the patient’s stent.39 7. In this case the Morphology mask will be subtracted from the Bool mask to simulate the wall thickness of the aorta. 3. However. Keep in mind that this is not the true thickness of the aorta but merely a visualization aid. use Edit Mask in 3D to get rid of the protrusions and then recalculate the 3D model. The erode broke any connections between the aorta and spine. Calculate a 3D model on high quality. 5. Need Help? Check out the Mimics User Community: http://uc. Zoom in on axial slice 106. Measure Distances Distances can be taken from one point to another point on a 2D image or along a 3D surface. Select the 3D model previously created in the Boolean operations exercise. 2. 1.materialise. This gives us a quick diameter for the aorta. Click once on the image on one side of the aorta and again on the other side. 3. 4. and then Measure This measurement tool measures the shortest path along a surface between two points. 6.88.com/mimics . Calculate a 3D model on high quality. Click on the top of the aorta and then the bottom to get a distance along its surface.40 4. Now click Measure Distance under ‘Tools’ in the main toolbar. In the ‘Measurements’ tab of project management click the New button Distance Over Surface. Your final result should be a 3D model of the heart.mcs’ dataset. 2.41 7. Perform the steps needed to threshold so that you have a mask for only the lungs. 3. Go to ‘Export’ in the main toolbar and select Txt…. and aorta.3 Homework Re-open the ‘heart_se. Select an output directory by clicking the folder icon . 1. create separate masks for the aorta and spine using Boolean operations. Create a 3D model. Next. spine.com/mimics . Hint: Think about what is inside the lungs and how you would threshold for this. Select the measurements you want to export and click ‘Add’. Save the project as “Lesson3_your name”. Need Help? Check out the Mimics User Community: http://uc. Export to txt Any measurements taken can be exported for further analysis. 3. lungs.materialise. 4. Click ‘OK’ to export the measurements to whichever output directory you have selected. Also segment the heart. Name the mask ‘Mandible’. Open the ‘skull_se. Click on Thresholding and select the predefined ‘Bone (CT)’ setting. Click on Cut with Polyplane under ‘Simulation’ in the main toolbar. fit and function. like with advanced engineering analyses. you can make cuts. This helps a surgeon validate their implant selection. Surgical Simulation Cut Cutting can be done in either 2D or 3D.1 Mimics’ Simulation module allows the simulation and planning of surgeries. After the anatomy is modeled. Professionals in the orthopedic and maxillofacial fields often prepare for their surgeries using this module. Need Help? Check out the Mimics User Community: http://uc. 5. import STL. If a portion of a patient’s anatomy is missing.com/mimics . 2. an implant design can be imported into the Mimics platform to test form. 4. As an engineer. Simulation also gives you the flexibility to test out different implant sizes and designs with a patient’s anatomy. After cutting and repositioning. 4. and analytically. in measurement studies for example. Just like in surgery. Split. soft tissue simulation demonstrates how the soft tissue will change with the modifications made. You have the ability to change the orientation and size of the cutting plane. The models created in Mimics can provide an engineer with a better understanding of the geometrical constraints in biomedical design. the mirror tool can be used to reflect the anatomy across a plane. 1. 4. Create a 3D model using high quality. 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.42 / Mimics Lesson 4: Surgical Simulation Explanation Tools to learn: Cut. Select Region Grow and then click on the mandible in the sagittal view. The procedures outlined below will show you how to accomplish these tasks. With the use of Mimics a design can be validated both geometrically.2 Step by Step Tutorial Scenario: You are a maxillofacial surgeon presented with a patient who has a diseased portion of the jaw and requires an implant.mcs’ project. 3.materialise. the simulation module aids in the design process. position an implant. split and reposition parts. click once behind the last molar and double click your second point at the base of the mandible. In the cutting plane properties dialog box you can change the depth. and extensions at the front and end of the cutting path. Adjust the points as needed to make the cut as vertical as possible. Click ‘Preview’ to view where the plane will cut and if everything looks okay. left click on the plane and the arrow will reappear. There is also a preview option to visualize how the plane will look with the specified dimensions.materialise. The plane itself can be moved by dragging the green points located on each end of the cutting plane.com/mimics . click ‘OK’ to apply. You can change the orientation of the cutting plane by dragging the red arrowhead. thickness. Select ‘Properties’ in the Cut with Polyplane dialog box. 8.43 6. Need Help? Check out the Mimics User Community: http://uc. If you cannot see the red arrowhead. To make a cut. 7. If the plane is not cutting where you want. readjust its dimensions. 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). 10. then click ‘OK’. 12. Make sure the jaw is selected under ‘Objects to Cut’ and your cutting path is selected. Click on Cut with Polyplane under ‘Simulation’ in the main toolbar to make another cut. Make sure ‘PolyplaneCutMandible’ is selected under ‘Objects to cut:’ and ‘CP2’ is selected under ‘Cutting paths:’. 11. Need Help? Check out the Mimics User Community: http://uc.com/mimics .44 9. Place your cutting plane behind your first cut. The cut will show up in the 3D objects tab as PolyplaneCut-Mandible.materialise. Click ‘OK’ when you are happy with the placement of the cutting plane. To view the jaw implant. Make sure ‘PolyplaneCut-Polyplane CutMandible’ and ‘Two largest parts’ is selected. After importing STL files. Select Reposition under ‘Simulation’ in the main toolbar. Click ‘OK’ and notice the middle portion of the jaw is removed. If you cannot see the jaw implant in your 3D screen. and then click ‘Open’. This simulates removing a diseased portion of the jaw. The distance you want to move in a specific direction can also be entered manually into the coordinate boxes.com/mimics . Import and Reposition an STL The jaw implant we will use is an STL file. Need Help? Check out the Mimics User Community: http://uc. you may need to zoom out to see where it is located. To move the implant to a particular spot (not along an axis). To move the implant in either the x. 14. you can grab the yellow rectangle at the origin of the axes. click on the eyeglasses next to ‘jaw_implant’ in the ‘STLs’ project management tab. 1. you would click on Load STL in the ‘STLs’ tab. select the STL of choice.45 13. 2. Choose Split under ‘Simulation’ to split the parts along the cuts. or z direction pull on the corresponding axis. the jaw implant is already available to you in the STL tab. y. you can use the repositioning tools to place parts in the correct anatomical location. Since the student edition of Mimics does not allow STL import. However to load an STL in the professional version of Mimics.materialise. Make sure the jaw implant is selected under ‘Objects to Reposition’ and click ‘Move with Mouse’. Grab each of the different rotation handles to become familiar with which ring causes rotation in which direction. Selecting ‘Go to home pos’ will move the 3D object to its original location. grab and move the yellow rectangle in the middle of the tool. make a cut that goes through the femoral head. 6.com/mimics . Save the project as “Lesson4_your name”. 5. you can move a 3D object to that position by clicking ‘Go to saved pos’. 4. Click ‘Rotate with Mouse’.mcs project’. Use the tools in Reposition to place the implant on the mandible as shown.46 3. Need Help? Check out the Mimics User Community: http://uc.materialise.3 Homework On the ‘femur_se. You can save the location of a 3D object by clicking ‘Save Position’ in the ‘Reposition the 3D Objects’ dialog box. To change the rotation center. The Move and Rotate tools can also be found in the ‘3D Objects’ tab. Split the cut and p osition the ‘femur_implant’ STL. 4. Once a position has been saved. 3. the data from the CT scans must be imported into CAD. Use Mimics to create an IGES surface. Crop the mask so it only contains the lower portion of the patient’s left knee. to a mask. These polylines can then be used to fill in a mask’s cavities or to fit freeform CAD objects. 4. 2. Iges Surfaces Export to CAD requires an Iges file.mcs’ dataset. The CAD objects created in Mimics can be directly exported as IGES files to any CAD program. 1. Mimics creates an STL surface mesh. The MedCAD module allows us to create IGES surfaces and curves based on the anatomical geometry from the scan. 5. Mimics can automatically generate the contours (or polylines) of a segmentation mask.1 The MedCAD module acts as a bridge between medical imaging and traditional CAD design. Before any design work can be done. Pro/Engineer. export to CAD. 5. Name the new mask “knee-1”. Select region grow and click somewhere on this mask. An important feature of MedCAD is the ability to work with polylines. IGES surfaces and curves.2 Step by Step Tutorial Scenario: As an engineer you need to design a standard implant for a partial knee replacement. Create a mask on the knees using lower and upper threshold values of 120 and 3071. such as SolidWorks.com/mimics . to relay all the information necessary to begin the implant design. like surfaces or spheres. but traditional CAD packages require a parametric surface file such as IGES. Open up the ‘knee_se. and Catia. Follow the procedures in the step by step section to learn how to perform these steps.materialise. Need Help? Check out the Mimics User Community: http://uc. which can be exported to CAD.47 / Mimics Lesson 5: CAD link Explanation Tools to learn: Polylines. Click on Cavity Fill from Polylines under ‘Segmentation’ in the main toolbar. This turns off the masks so that they are not displayed in the images. Make sure the ‘knee-2’ mask is active. scroll up through the slices looking for breaks in the ‘knee-2’ mask. 6. . this tool fills in all small holes of a mask that are encompassed by a larger boundary polyline. You will notice the first break on slice 57. 10. Need Help? Check out the Mimics User Community: http://uc. 7.materialise. Under ‘Segmentation’ in the main toolbar click Calculate Polylines mask and click ‘OK’. Select the ‘knee-1’ When Mimics calculates polylines it creates a contour around the selected mask on each slice. Calculate a 3D model of ‘knee1’on high quality. Cavity Fill from Polylines is useful when a mask has many small holes that need to be filled in. 8. Make sure ‘Fill Cavity of: Set 1’ and ‘Using Mask: <New Mask>’ are selected. Click ‘Apply’ and then ‘Close’. On each slice. 9.48 5.com/mimics . You will notice a lot of holes in the mask which means editing must be done. Zoom in on the left knee in the axial view. Click on the eyeglasses in the project management ‘Masks’ tab under the ‘Visible’ column for all of the masks except ‘knee-2’. The polyline set you just created will show up in the ‘Polylines’ tab of project management. Name the new mask “knee-2”. Starting at axial slice 0. Go to Edit Masks and select ‘Draw’. 96.com/mimics . Need Help? Check out the Mimics User Community: http://uc. Draw in a connection where there is a break in the mask. 90. You want ‘Fill Cavity of: Set 2’ and ‘Using Mask: <New Mask>’. 78. Select Cavity Fill from Polylines . (Breaks occur on slices 60. 87. 12.materialise. 99) 14. Under ‘Segmentation’ in the main toolbar click Calculate Polylines mask and click ‘OK’. Rename this mask “knee-3”. 93.49 11. 15.75. calculating a new set of polylines will create contours that include all the areas you just edited. Select the ‘knee-2’ Now that all the breaks have been filled in. . Scroll up through the slices continuing to fill in any breaks. 13. 84. 17. Calculate a 3D model on high quality. A dialog box will appear saying there are no polylines created for the current mask and asks if you want to create them.materialise. go to the slice where there is still a hole. Update the polylines by clicking Update Polylines under ‘Segmentation’ (or use the shortcut ‘Control+u’). Now. In this case. Notice that this 3D model is much more complete than the first one calculated. Now the ‘knee-3’ mask should no longer contain the kneecap. Click ‘Yes’. using the green up arrow of ‘Copy to slices’ in Multiple Slice Edit . Delete the kneecap. which can be seen in axial slices 39 through 93.com/mimics . Draw in a connection on the most recent mask using Edit Masks. You may need to select more of the kneecap as you copy to each slice. we can use editing to erase the knee cap and the remaining portion of the femur. Since we are only going to look at the bottom portion of the knee (tibia). If the holes are not filled then you missed a break somewhere in the mask. Perform another cavity fill from polylines but select ‘knee-3’ for ‘Using mask:’. Need Help? Check out the Mimics User Community: http://uc. the break should be filled in. 16.50 All of the holes within the mask should be filled. 102. Start at axial slice 0 and click on the outer contour of the ‘knee-4’ mask. Name this polyline set ‘polyKnee’. the polylines are automatically added to the current polyline selection. ‘Keep Originals’ and set ‘Correlation(%)’ to 97. Click on the ‘knee-4’ mask and then press ‘OK’. Check ‘Auto multi-select’. A polyline selection is a portion of a polyline set. Do a Region Grow and name the new mask “knee-4”. Click Polyline Grow under the ‘Polylines’ project management tab. Select ‘From: polyKnee’ and ‘To: New Set’. You can also drag a box around the knee.com/mimics . Need Help? Check out the Mimics User Community: http://uc. Use ‘Erase’ of Edit Masks to erase the extra area of bone above the tibia on axial slices 99. The contour will be highlighted when you place your mouse over it. If the polyline’s shape is within the correlation percentage’s limits (within 97% similar). 19. Next.materialise. You should no longer see the kneecap or extra bone above the tibia. Polyline Grow looks at polylines above and below the selected slice.51 18. 21. 22. Select Calculate Polylines. calculate a 3D model. 20. and any other slices above 102 that you may have included when you cropped the mask. 52 23. Select Grow Polylines with ‘From: polyKnee’ and ‘To: New Set’. up through axial slice 96 (you will need to reselect on at least slices 51. 25.materialise. If we did not do this editing there would be a gap as shown in the picture on the right. as needed. In order to be able to add a polyline. 57. While on slice 96. the shape must resemble the previous contour. we can add an additional contour to the polyline set.com/mimics . Scroll upwards until you get to a slice where you need to reselect which polyline you want to grow (slice 48). and 102 select the left most contour. and 60 and maybe more). select Update Polylines 26. We must break this connection so that later when we are growing polylines. 99. Need Help? Check out the Mimics User Community: http://uc. Continue reselecting. under ‘Segmentation’. 24. On axial slices 96. Use ‘Erase’ of Edit Mask to break the connection on axial slice 96. 30. Also. We need to turn these separate contours into one surface because an IGES curve cannot be fit to multiple contours. Select Grow Polylines with ‘From: polyKnee’ and ‘To: New Set’. Need Help? Check out the Mimics User Community: http://uc.53 27. Repeat this procedure for the last two selections in the ‘Polyline set’ list. you need at least three contours in a set to fit a surface on. Select the first set under the polyKnee set (‘Selection 5’ in the picture on the right however your number may be different). Now we have three polyline selections that are suitable for fitting a surface on.materialise. In the main toolbar under ‘MedCAD’. 99.com/mimics . Look at the 3D view to see how these selections look as surfaces. If the set contains more than one contour per slice a surface cannot be fit. There are some holes in the surface at the top of the knee but the overall anatomical shape is correct. The u-parameters and v-parameters are automatically calculated for you. Save this file as “Iges Knee”. On axial slices 96. 28. Make sure you have at least 30 control points and click ‘OK’. and 102 select the right most contour. click ‘Freeform Surface’ then click ‘Fit from Polylines’. 29. You will know if a set is good to fit a surface on because the ‘Surface Fit Parameters’ box will say ‘Set OK’. These holes can be stitched and filled in CAD to create a solid part. then click ‘IGES…’. Click ‘Finish’ to export the surfaces.2. Press ‘Add’.materialise. 2. Select an ‘Output Directory’. 3. Select ‘Export’ in the main toolbar.com/mimics . and 3. Need Help? Check out the Mimics User Community: http://uc.54 Export to CAD The surface created in the above exercise can be exported to CAD. Click the ‘CAD’ tab and highlight surfaces 1. 1. On axial slice 55 you need to break the connection between the femur head and greater trochanter to be able to add polylines. You will also need to use editing to add a contour on the top of the trochanter (on axial slice 65) so that you have enough contours in the set to fit a surface. Hint. trochanter and head.3 Homework Open the ‘hip_se. Remember polylines must be added to correct unwanted gaps that would otherwise exist. Need Help? Check out the Mimics User Community: http://uc.55 5.com/mimics .mcs’ dataset and create an IGES surface for the femur shaft.materialise. 1. and hydraulic diamater. Cut Centerline Ending.com/mimics . Tools exist to gather data about these centerlines such as maximum and minimum best fit diameter.2 Step by Step Tutorial Scenario: As an engineer designing a stent.56 / Mimics Lesson 6: Centerline creation Explanation Tools to learn: Calculate Centerline. Open the ‘hip_se. Need Help? Check out the Mimics User Community: http://uc. tortuosity. Name the mask “Centerline” and create a high quality 3D model. Use Mimics to calculate the centerline of the aorta and prepare the endings of the centerline for CFD. and airways. (Axial slice 335 shown) 3. centerline measurements. 2. curvature. Centerlines can be modified within Mimics to optimize the inlets and outlets for various analyses like CFD. take measurements based on these centerlines. you need to analyze fluid flow through the aorta. and export the corresponding values. 6.1 Mimics allows for the determination of centerlines for any type of branching including arteries. veins. Calculate and Export Centerline You can find the centerlines of veins and arteries. The procedures outlined below will show you how to accomplish these tasks.materialise. export centerlines to CAD. 6.mcs’ dataset. Perform a threshold with values 174 to 279 and then a region grow on the aorta. 57 4. To better visualize the centerline click on the transparency button the 3D toolbar. Need Help? Check out the Mimics User Community: http://uc. 5. This is 2 by default. Leave the default fitting parameters and click ‘OK’. in The red dots on the centerline indicate bifurcation points. Distance between control points sets the distance between each point of calculation along the vasculature.materialise. Select Fit Centerline under ‘Freeform Tree’ in the ‘MedCAD’ section of the main toolbar. Number of iterations is the amount of times you want the algorithm to run. which is fine in most cases.com/mimics . 6. All of the vessels in this dataset are bigger than 1 mm so we will leave the default value. Highlight the mask of the 3D model of the artery. Resolving resolution is the minimum detail you want Mimics to use in its centerline calculation. 58 7. Select ‘Text File (*. click on the eyeglasses of whichever branches you want to hide. Highlight all of the branches by holding the control key while selecting each branch. The properties dialog box contains information about the centerline and its branches. Click ‘Export’. Another way to take measurements is through New ‘Measurements’ project management tab. Select the ‘CAD Objects’ tab in the project management toolbar and click Properties . Besides changing the color of the centerline you also have the option to delete branches. in the The bottom half of the list deals with centerline measurements. 9. Need Help? Check out the Mimics User Community: http://uc. These can be exported to programs such as Excel or Matlab for further analysis depending on the application. 12. 11. Leave only ‘Best fitted diameter’ checked and click ‘Save’. The text file contains the coordinates of the points and the selected measurements. Click the yellow folder to select an output directory.materialise. Go to the ‘Measurements’ tab and click New . Name the file “Aorta centerlines”.txt)’ for ‘Save as type:’. You can export to a text file or as an Iges. To export to Iges select IGES… under ‘Export’ in the main toolbar and select what you want to export under the CAD tab. To change which branches are visualized.com/mimics . To see a definition for each of these measurements see the ‘Centerline Measurements’ section of the ‘MedCAD menu’ help files. 8. 10. The 3D objects tab will have the modified centerline (displaying how it looks with the cuts). Go to Actions of the ‘CAD Objects’ project measurement tab. click on the top branch of the artery to make a cut. As you move your mouse along the centerline.materialise. 4. 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. Select one of these measurements and put your mouse over the 3D model of the centerline to see the measurement’s value. the values are updated for the measurement until you click on a point. . 5. Repeat this for a few of the measurements. Highlight ‘Centerline 1’ and click ‘Indicate’. 1. Select Cut Centerline Ending 3. 2. On the 3D model.com/mimics . Click ‘OK’.59 13. Make a few cuts on different branches to get familiar with the tool. Need Help? Check out the Mimics User Community: http://uc. Need Help? Check out the Mimics User Community: http://uc. 1. select two control points on either side of the green control point to indicate the boundaries of your change. These will turn black. Next. 2. You can modify a centerline by moving the control points. This is useful when the calculated centerline does not follow the accurate branching of a vessel and needs to be adjusted. It will turn green.materialise. 3. Go to the CAD Objects menu.com/mimics . Double-click to finalize the change. Drag the green control point to the desired location until it is in the position that you want. Select a control point you wish to change. Select the Actions button and then ‘Edit Centerline Control Points’.60 Modify Centerline Modify Centerline provides the ability to reposition centerline control points. 4. Calculate the centerline.mcs’ dataset.61 Notice that now the centerline has less curvature than it did originally.materialise.3 Homework On the ‘heart_se. Need Help? Check out the Mimics User Community: http://uc. 6. best fit diameter. segment a couple of the small branches coming off of the heart. and maximum and minimum diameters for these branches.com/mimics . 7. Material Assignment. reducing the number of triangles to enhance the calculation speed during FEA.1 The FEA module of Mimics allows optimization of triangle meshes to prepare for further analysis using FEA or CFD. Need Help? Check out the Mimics User Community: http://uc. and optimizing triangle quality. export to FEA. creating a volume mesh.materialise. The typical process for remeshing includes smoothing the mesh to remove sharp edges that may act as unwanted stress risers in analysis.62 / Mimics Lesson 7: FEA (part 1) Explanation Tools to learn: Remeshing. The following picture shows an example of a mesh before and after it has been optimized. Remeshing is used to increase and optimize the quality of triangles and preprocess a model for analytical packages.com/mimics . the inspection scene. and sketch created. surface. The tab next to 3D view. and the operations and properties section. the database and inspection page section. The database page gives you information about each part. Need Help? Check out the Mimics User Community: http://uc. The inspection page allows you to control all your remesh operations and to inspect and visualize the quality of your mesh. You can use the database tree to select various objects for a specific operation. The upper right box includes the database and inspections page. etc.com/mimics .materialise. The operations page shows all the parameters available to change when applying an operation to your object. curve. surface area. color. The 3D view allows you to see the 3D model of the part you are working on. The properties page will show you all properties (such as number of triangles. is where you can visualize the triangulated mesh corresponding to your part. The operations page for the smooth tool is shown below as an example.63 The Mimics remesher is broken up into a few main windows.) associated with a selected object. A list of all the steps and operations you complete is available in the log window. the log window. volume. these include the 3D view. 64 Once FEA meshes are created. 7. FEA Remeshing Remeshing is used to increase and optimize the quality of triangles for the preprocessors of analytical packages.com/mimics . Select ‘Femur’. Leave the smoothing parameters at the default settings. 2. and then click on the 3D model of the femur. Open up the ‘FEA_femur_se. Go to the ‘Remeshing’ tab located at the top of the Remesher.materialise. In order to prevent the bottom of the femur from being rounded we must check preserve sharp edges. 3. The ability to assign material properties comes from the close correlation between the density of a CT image and the density of anatomical materials. Highlight the ‘Femur’ in the ‘3D Objects’ tab of the project management toolbar.mcs’ project. Click the Smooth button 6. The procedures outlined below will show you how to accomplish these tasks. 4. Prepare the hip dataset for FEA using the Mimics remesher and then assign material properties to your mesh based on the grayvalue information in the CT scan. Need Help? Check out the Mimics User Community: http://uc. Mimics can assign material properties based on Hounsfield units and export to FEA packages directly. 5. Check ‘Preserve sharp edges’ under ‘Advanced Options’ and click ‘Apply’.2 Step by Step Tutorial Scenario: You are asked to perform finite element analysis to explore the biomechanics associated with the hip. Model navigation works the same in the remesher as in normal Mimics. 1. Click the Remesh button in the same tab. like bone. 7. We use compensation to counteract any shrinking that might occur as a result of the smoothing algorithm. Need Help? Check out the Mimics User Community: http://uc. When an angle is larger than the flip threshold angle the triangles comprising the angle may not be reduced. Geometrical error is the maximum deviation allowed between the original surface and the new one. Click Auto Remesh in the ‘Remeshing’ tab and make sure ‘part’ is selected for ‘Entities’.com/mimics . it may be that there is a little deviation in position.materialise. Preserve surface contours should be used when there are surfaces defined that are not based on the part geometry. 2 triangles are replaced by one triangle.09 and leave the rest of the default reducing parameters.65 The higher the smooth factor the more smoothing will be applied.09. 9. Select the Reduce button in the ‘Remeshing’ tab and click on the part selecting ‘Femur’. 8. with a value of 1 applying the most smoothing. If during the process of reducing. Number of iterations is the amount of times the smoothing algorithm will be applied.715 mm making the geometrical error about 0. It is recommended to use 1/8 of the pixel size to maintain accuracy between scanner data and models. If there is no critical edge then the angle value is the maximum angle that can be created during reduction. Click ‘Apply’. so in our case the pixel size is 0. Leave preserve surface contours unchecked. Change ‘Geometrical error’ to 0. Select ‘Height/Base (N)’ for ‘Shape Measure’ in the ‘Inspection Page’ tab. 13. Some of the auto remesh parameters include shape quality threshold which sets the desired quality of triangles. We want all of the triangles to be above the 0. we have the flexibility to increase the maximum geometrical error to 0. Need Help? Check out the Mimics User Community: http://uc. Click Quality Preserving Reduce Triangles in the ‘Remeshing’ tab then click on the part.4. This step reduces the amount of triangles while preserving the quality. and set ‘Maximal edge length’ to 5.3. and leave the rest of the default parameters.materialise. maximum geometrical error which is the maximum deviation between the part’s surface before and after automatic remeshing.2.3 shape measure threshold we set because triangles with a quality lower than this will not import into FEA or CFD packages. The histogram is measuring the quality of all triangles in the mesh. set the ‘Maximal edge length’ to 5.3. You can visualize shape measure on the histogram by changing ‘Current Measure’ to ‘Shape Measure’ under ‘Histogram Parameters’. Large models with many low quality triangles can be better remeshed in incremental steps. Click ‘Apply’. Change the minimum and maximum values to 0 and 0. Leave the rest of the default parameters and click ‘Apply’.1. 12. check ‘Control triangle edge length’. sometimes it helps to use a shape quality threshold of 0. then 0. and then 0. and maximal edge length which sets a limit on the length of edges of triangles created.66 10.com/mimics . A rule of thumb is to keep the geometrical error used in reducing the same as the maximum geometrical error. 11. Change the ‘Maximum geometrical error’ to 0. With this example. Check ‘Control triangle edge length’.4 so we can increase computation time by reducing the number of triangles. With this tool the software determines the parameters automatically.67 Your model should resemble the femur in the picture shown above.com/mimics . 2. This allows us to have a surface mesh and a volume mesh when we go back into Mimics. bring the volume mesh back into Mimics and then assign material properties. If you wanted to load a mesh rather than create one. manually performing the steps allows more control over the parameters. The Remesh Wizard can be used to achieve nearly the same results as the steps we’ve done so far. under the ‘FEA Mesh’ tab of Need Help? Check out the Mimics User Community: http://uc. however. 1. you would click Load Mesh project management.materialise. You can create a volume mesh in the remesher. Material Assignment Mimics assigns materials to volumetric meshes based on Hounsfield gray values. Duplicate the ‘Femur’ by right-clicking and selecting ‘Duplicate’ under the Active Scene tab. Select Create Volume Mesh in the ‘Remeshing’ tab. ‘Shape measure’ to ‘Aspect ratio (A)’. 6. Turn on only the volume mesh in the 3D pane.materialise. Aspect ratio is a common mesh analysis for FEA. and ‘Shape quality threshold’ to 25. The volume mesh can be found in the ‘FEA Mesh’ tab. with Init and Refine. 4. Make sure ‘Femur’ is selected as ‘Entity’. Control edge length limits the tetrahedral elements to the dimension you set. 5. It is good to set the shape quality threshold to at least 25. Click the glasses under ‘Contour Visible’ in the ‘FEA Mesh’ tab to view where the mesh is located in 2D. 7. For example. The surface mesh can be found in the ‘3D Objects’ tab and its name will start with the word ‘Remeshed’. The mesh parameters allow you to define certain details of your mesh. since thresholds below this are considered poor quality and not accepted by most FEA packages.com/mimics . or fill the volume and fit the tetrahedrals more appropriately . Click ‘Apply’. the method used to create the tetrahedral volume mesh can either fill the volume. Set ‘Method’ to ‘Init and Refine’.68 3. Need Help? Check out the Mimics User Community: http://uc. as with Init. The mesh quality options define how Mimics analyzes the mesh. Close the remesher to return to Mimics by clicking the . 9. 11. Leave ‘Limit to Mask: None’.materialise. Scroll through the 2D axial and sagittal views to visualize the internal distribution of the mesh. Click Enable/disable clipping . Make sure ‘Uniform’ is selected under ‘Method’ and set the number of materials to 15. In the ‘Clipping’ tab. Need Help? Check out the Mimics User Community: http://uc.com/mimics . Click ‘Yes’ to the dialog box that pops up. check the ‘Axial’ and ‘Sagittal’ boxes under ‘Active’. This message explains that Mimics needs time to calculate the average gray value for the pixels of each element of the mesh.69 8. 10. Press the Materials icon. Set the ‘Texturing’ to ‘None’ for both. Select ‘OK’. In the ‘Use material expressions’ section you can manually enter known expressions for properties.70 The uniform method divides the range of gray values into equal sized intervals based on the number of materials you picked. Enable clipping in only the coronal view and set ‘Texture’ to ‘None’. Click on the ‘Material Editor’ tab. 12. Click ‘Cancel’. select an output format.materialise. 2. 1. This is where you can enter properties for materials such as density. 14. Selecting ‘Materials’ under the Histogram tab allows you to preview these intervals.com/mimics . Scroll through the coronal view to see the internal material distribution. click ‘Add’. Export to FEA Meshes created or modified in Mimics can be exported for further analysis in FEA packages. A list of such expressions can be found in the help files by clicking the contents tab> Mimics Modules> FEA> Empirical Expressions. and then select ‘OK’. Click Export Mesh in the ‘FEA Mesh’ tab. You would select the name of the mesh you want to export under the Mesh tab. Need Help? Check out the Mimics User Community: http://uc. 13. 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. Need Help? Check out the Mimics User Community: http://uc. create an optimized surface mesh of the knee.71 7. Following the same procedure used to remesh th e hip.materialise.com/mimics .mcs’ file.3 Homework Open the ‘knee_hw_se. 2 Step by Step Tutorial Scenario: You would like to research the stresses associated with a jaw implant using FEA. Open the ‘skull_se. 8. the FEA module of Mimics can generate non-manifold assemblies. 1. Name the mask “Mandible”. create and split a non-manifold assembly. is identical.mcs’ project. 8. 2. Non-Manifold Assembly Creating a Non-Manifold Assembly Non-manifold assemblies are created to make sure the common surface between parts.72 / Mimics Lesson 8: FEA (part 2) Explanation Tools to learn: Wrap. To accomplish this. Perform a threshold and region grow to segment the mandible. Calculate a 3D model. The procedures outlined below will show you how to accomplish these tasks. You first want to analyze the implant and bone as a single mesh and then later as two separate meshes. also called the lower left first molar. you can split the bone and implant mesh into two separate meshes using the splitting tool. 3. This is necessary to perform accurate FEA. or t-sections. Remember to do a region grow and recalculate the 3D model after you are finished editing. Once an assembly is created the entire mesh can be optimized for FEA in the remesher. Use Mimics to create these meshes.com/mimics . Use Edit Mask in 3D to remove the second from the last molar on the patient’s left side of the jaw. mating parts need node to node matching. Need Help? Check out the Mimics User Community: http://uc.1 When running an FE analysis on multiple parts.materialise. Nonmanifold assemblies create matching surfaces between parts such as between bone and implant. like between an implant and bone. This final step creates the two separate meshes with a node to node matched surface. After remeshing is complete. 4. 73 5. 6.materialise. Turn on the ‘tooth_implant’ STL. 10. Turn off Clipping. The Wrap tool in the Remesher can be used to fill in the holes of the 3D model. Turn on Clipping in the 3D Toolbar. Position the implant so it fits into the socket created in step 4 when you removed the tooth. 9. 8. check the box next to ‘Sagittal’ under the ‘Active’ column. Need Help? Check out the Mimics User Community: http://uc. This is an especially useful tool for FEA where holes can cause inaccurate results. Change the ‘Texturing’ to ’None’ by clicking on the word under the texturing column until it says ‘None’. 11.com/mimics . In the ‘Clipping’ tab of project management. Scroll through the 2D sagittal images and notice that in the 3D view there are some holes in the model. 7. com/mimics . 15. Gap closing distance determines the size of gaps that will be wrapped. In the ‘Active Scene’ tab. 13. 16.2 and ‘Smallest detail’ to 1. Check the help files for details on the other wrap parameters. Go to the ‘3D View’ tab in the remesher. Click ‘Apply’. Repeat this for the ‘tooth_implant’ so that only the wrapped 3D models are displayed in the 3D view. Smallest detail sets the size of the triangles of the newly created surface. Select Wrap in the ‘Fixing’ tab. Select the ‘Mandible’ and ‘tooth_implant’ as ‘Entities’. 17.materialise. right-click the ‘Mandible’ and select ‘Hide’. Select both the tooth_implant and the mandible with the removed tooth. Leave the rest of the default parameters. 18.74 12. Choose ‘Remesh’ under ‘FEA/CFD’ in the main toolbar. 14. 19. Click ‘OK’. Set ‘Gap closing distance’ to 0. Need Help? Check out the Mimics User Community: http://uc. Choose the Create Inspection Scene tool under the ‘Remeshing’ tab. Now we can create a non-manifold assembly. 23. In the ‘Standard Section-X’ tab.materialise. 21. 25. Click on ‘Intersecting entity’ then leftclick the ‘tooth_implant_wrapped’. check the box next to ‘Clip’ to enable clipping. 26. In the ‘Remeshing’ tab click Create non-manifold assembly .com/mimics . Click the plus sign next to ‘Section List’ in the ‘Active Scene’ tab and then click ‘Standard Section-X’. Need Help? Check out the Mimics User Community: http://uc. Move the scrollbar and check the 3D view to ensure all holes have been filled in from the wrap.75 20. The wrapped model should contain no holes in the location where the original model did. Click ‘Apply’ to combine the mandible and implant meshes. 24. Left-click on the ‘Mandiblewrapped’ to select it as the main entity. 22. Click ‘Position’ and a scrollbar will appear. Click ‘Apply’. and ‘Filter mode: Collapse’. 28. This can also be selected from the database tree. Left click on the 3D model and select ‘Mandible_wrapped_non-manifold_assembly’. Optimizing the Non-Manifold Assembly Mesh We want to create an optimized mesh just as we did for FEA remeshing. Sharp triangles must be removed because they are detrimental to the quality and speed of FEA.com/mimics . Click ‘Apply’. 2.2000’.materialise.000’. Select the ‘Mandible_wrapped_nonmanifold_assembly’ for ‘Entity’ in the create inspection scene tab. Click the Filter Sharp Triangles tool in the ‘Fixing’ tab.76 27. 1. Need Help? Check out the Mimics User Community: http://uc. Set the ‘Filter small triangles parameters’ to ‘Filter distance: 0. ‘Threshold angle: 15. 7. 9. Leave the other parameters at the default settings and click ‘Apply’. 4.3.com/mimics .06 and check ‘Preserve surface contours’. In the ‘Inspection Page’ tab. Make sure the slider on the histogram is at 0. Check ‘Preserve sharp edges’ under ‘Advanced options’ and leave the rest of the default parameters. 6. 5. Left click on the 3D model and select the Mandible_wrapped _non-manifold_assembly’s ‘Surface’.materialise. Since the 3D model will only be used for FEA you can reduce the amount of detail of its outer surface by smoothing. Need Help? Check out the Mimics User Community: http://uc. Click Auto Remesh in the ‘Remeshing’ tab. Click ‘Apply’. select ‘Height/Base (N)’ in the ‘Shape measure’ dropdown under ‘Quality parameters’. the quality needed to generate a volume mesh. Make sure ‘Shape Measure’ is selected for ‘Current measure’ in ‘Histogram parameters’. Select Smooth in the ‘Remeshing’ tab.77 3. There are too many triangles for Finite Element Analysis so a reduction is necessary. ‘Geometrical error’ to 0. Set the ‘Flip threshold angle’ to 30. Click Reduce then left click on the 3D model to select ‘Mandible_wrapped_nonmanifold_assembly’. 8. Set the ‘Maximum geometrical error’ to 0. Quality preserving reduce triangles removes the groups of small triangles still contained in the mesh. 11. Change the ‘Maximum geometrical error’ to 0. if we limit the maximum edge length we can create a uniform mesh. 13. Need Help? Check out the Mimics User Community: http://uc. Leave the other parameters the same. The final result is a uniform mesh with the desired quality.1 and uncheck ‘Control triangle edge length’.materialise. Apply auto remesh again after checking ‘Control triangle edge length’. Click Quality Preserving Reduce Triangles in the ‘Remeshing’ tab. Click ‘Apply’. 12. Click ‘Apply’.2 and leave the other default parameters. Leave the other parameters at the default settings.com/mimics . Since the first auto remesh left the mesh containing triangles of divergent sizes.78 10. Exit the remesher to return to Mimics. Click ‘Apply’. If you wanted to export the remeshed 3D objects you would select the objects to be exported. 1. 3.materialise. and then click ‘Add’ in the Export menu.com/mimics . select the correct output format. 4. Need Help? Check out the Mimics User Community: http://uc. Select the Split non-manifold assembly tool in the ‘Remeshing’ tab. 2.79 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. Go to the 3D view and select the ‘Mandible_wrapped_non-manifold_assembly’ for ‘Entities’. 1. then split the assembly.08 and maximum geometrical error at 0. it should have been saved as ‘IGES knee’.materialise.3 Homework Use the 3D knee model you created in Mimics Lesson 5: CAD link.com/mimics . Hint.80 8. Create a non-manifold assembly of the knee and the knee_implant STL .Run your geometrical error at 0. Need Help? Check out the Mimics User Community: http://uc. com/mimics . Thank you for using Materialise’s lab book for your learning experience. MI 48103 734-662-5057 www.com Need Help? Check out the Mimics User Community: http://uc.materialise. If you would like more information about any of the Materialise software please contact us at: Materialise 3009 Miller Rd Ann Arbor.com [email protected] You now know how to utilize the tools in Mimics to transform 2D data into 3D models.materialise.