CHAPTER 1: IMPORT. 5 CHAPTER 2: MIMI. 11 CHAPTER 3: SIMON. 25 CHAPTER 4: HIP. 39 CHAPTER 5: OBTURATOR. 47 CHAPTER 6: MANUAL IMPORT.

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1 Tutorials

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3 Table of Contents CHAPTER 1: IMPORT... 5 CHAPTER 2: MIMI CHAPTER 3: SIMON CHAPTER 4: HIP CHAPTER 5: OBTURATOR CHAPTER 6: MANUAL IMPORT CHAPTER 7: SIMULATION TUTORIAL CHAPTER 8: FEA TUTORIAL CHAPTER 9: CFD TUTORIAL CHAPTER 10: NON-MANIFOLD ASSEMBLY TUTORIAL i

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5 If you have chosen to install the demo files during the Mimics installation procedure, only two of the files used in this tutorial will be put in the MedData folder. The others can be found on the CD or can be downloaded from our website ( ). You will need to register first or, if you are already registered, sign in using your address. On the first page choose Mimics and follow the link to Tutorial Datasets. The extra tutorial files are a self-extracting zip-file. To unpack the file, double click on it and choose your MedData folder as destination folder. The following tutorials are available: Chapter 1: Import Chapter 2: Mimi Tutorial that shows how you can import images in Mimics Tutorial that shows how to do a basic segmentation and 3D calculation. Chapter 3: Simon Tutorial that shows some advanced segmentation functions to remove artifacts. Chapter 4: Hip Chapter 5: Obturator Chapter 6: Manual Import Chapter 7: FEA Tutorial Tutorial that shows how to use the MedCAD module. Tutorial that shows how to make a mold of a cavity by segmenting the Soft tissue around the cavity. Tutorial that shows how to use the manual import function. Tutorial that shows how to use the FEA module. Chapter 8: Simulation Tutorial Tutorial that shows how to use the Simulation module. Chapter 9: CFD Tutorial Chapter 10: Non-manifold Assemblies Tutorial that shows how to use the FEA module for linking to CFD. Tutorial that shows how to combine two meshes. 3

6 Table Of Contents Note: In Mimics you have the possibility to use both Hounsfield and Grey Values. This is very important when setting a threshold and when you use the Profile Line function. To switch between these two possibilities, go to Options > Preferences, General tab and select the Pixel unit you want to use. Most tutorials need one or more modules of Mimics (STL+, RP Slice, MedCAD, Simulation or FEA). If you wish to try that section of the tutorial and you don t have the required module(s) installed, an evaluation period of that module can be obtained on request. 4

7 Chapter 1: Import The goal in the first part of this chapter is to teach you how to import images and convert them into a Mimics project. The second part will illustrate how to organize the images in the project you made. In this tutorial we will discuss three topics: How to do an Automatic Import How to organize images How to do a Semi-Automatic Import Note: To import images from a tape you need to use the Dump Tape function Note: There are 3 ways to import images, depending on their format: automatic import, when the format of the files is known to Mimics semi-automatic, e.g. Bitmap or Tiff images manual import (Case 6), when the file type is unknown and you need to specify some parameters manually 1. Automatic import To start the Import wizard, first select File and then choose Import Images. An Import Project Wizard will be displayed where you can select where the images to be imported can be found (STEP 1). In the import wizard, browse to the MedData folder and select the folder called Import1. A list of files will be displayed in the Filename column and all the files will be automatically selected. Click the Next button. If the format of the images is known to Mimics (see the general help files for a list of known formats), you can select the images and press the Next button. If you click on the import information button, an import message will be displayed containing the correct path and format of the images. Note: In this case the file type is recognized, but in some cases the message log tells you that one or more images are of an unknown file type. If this happens, you have to perform a manual import (see Case 6). 5

8 Table Of Contents Note: If you want to keep all the files, press the Next button, otherwise first change the selection of images to fit your needs. This selection can be done in two different ways: either you can click on the first file and then on the last one you want to include while keeping down the Shift button (this way you will include all files in the interval) or you can select the files one by one while keeping down the Ctrl button. After clicking on the Next button you will reach the second step of the Import Project Wizard, in which you need to select the studies to be converted. The study you have just imported is already selected by default. In this window some information about the project can be found, such as the number of images, pixel size, patient name, orientation parameters, etc. 6

9 Mimics Tutorial Now you can click the Convert button and you will see a progress bar. During the conversion process, the project will be opened automatically displaying the Change Orientation window since one or more of the orientation strings were missing in the original images. 7

10 Table Of Contents Now you need to set the Orientation Parameters that are missing and change the ones that are incorrect. Actually if you look at the axial image you see the orientation strings L and R, which stand for Left and Right respectively together with A and P which stand for Anterior and Posterior. In the coronal and sagittal image two Xs are displayed instead of the above mentioned orientation strings. Move the mouse cursor to the top X in the sagittal or coronal image. The cursor shape changes to a hand and if you right-click, a menu appears with all possible orientation strings. Select Top. Note that all the other orientation strings are completed automatically. If the orientation of the images is right you can click OK and your Mimics project will be opened. Now you can process your images using the tools explained in the tutorials dealing with Case 2 and Case 3 (Threshold, Region Growing, Edit, etc..) 2. Organizing images Once you have opened your project, you can decide to exclude some images if they are not good or if you don t need all of them. For example, we can decide to delete the images of the project Simon.mcs that don t include parts of mandible or that don t contain any information. To access the Organize Images window, go to File and then choose Organize Images. 8

11 Mimics Tutorial First of all you can get a better look at the images changing the preview size to Medium or Large by selecting the respective size from the Preview size dropdown box. If you look at the images you will notice that the ones that correspond to table positions 49.5 and 48.5 do not contain any information about mandible. So you can click on these two images to unselect them, the green mark will disappear and the image will be unchecked in the list on the left. On closer inspection you can also notice that the image at table position 1.5 is the last one that contains information about the mandible. Right-click on the image at position 1.5 and choose Unselect after this. All the consecutive images will be unselected also. Press OK and scroll through the axial images to check if the correct ones are visible in the project, you should not see the ones you unselected. You can now save your Mimics project with the name Organizing Images.mcs going to File and then Save As. After you have done this you can make a segmentation following the next tutorial (Case 2) 9

12 Table Of Contents 3. Semi-automatic import Now we will try to import the Bitmap images you can find in your MedData directory in the "Import2" subdirectory. Again select File > Import Images and browse to the C:\MedData\Import2\ directory. If you press the Next button, a new window will be displayed. The only information you need to provide/change is the slice distance and the pixel size. This information should be collected by someone who is familiar with the machine used to make the CT-Scan. It is very important to insert the exact values since the dimensions of the volumes and the 3D depend on them. When the correct information is filled out, you can press OK to continue with the second step of the Import Project Wizard. Now the import continues in a similar way to the automatic import. You will need to select the study you wish to convert and your Mimics project will be created after clicking on the Open button. Now you should be able to set the orientation parameters as described in the previous paragraph and calculate a good 3D. 10

13 Chapter 2: Mimi In the second case of this tutorial we will show you some basic features of Mimics. The topics that will be discussed are: Opening the Project Windowing Thresholding Region Growing Creating a 3D representation Displaying a 3D representation STL+ Procedures Generating a STL file RP Slice procedures Generating a contour file Generating supports View of the end result 1. Opening the project From the File menu, select Open (Ctrl+O). The Open dialog box shows all projects in the working directory. Double click on the mimi.mcs file (Mimics project file). All images are loaded and displayed in three views. The view on the right shows the images as they are exported by the scanner (xy-view or axial view). The upper left corner is a reslice of these images in the xz-direction (xz-view or coronal view) and the bottom left is a reslice in the yz-direction (yz-view or sagittal view). The different colors of the intersecting lines refer to the colors of the contour lines of each view so every line refers to the slice in the corresponding view. You can easily navigate through the images by clicking on any point of the CT images in any view: the intersecting lines will move crossing each other in the point you clicked and all the views will be updated showing the corresponding slices. 11

14 Table Of Contents If you need to change the orientation of a view, go to File > Change Orientation. This will open a window in which you can change the orientation parameters simply by clicking on it with the right mouse button (see tutorial Case 1). Every indicator can be turned off by selecting View > Indicators in the Menu Toolbar. In the right border of the window you will see a slider that allows you to scroll through the images from the active view. 12

15 Mimics Tutorial In our current project (Mimi), all images are correct. If, however, you have an image set from which you want to remove some images, go to File > Organize Images. There you can add or remove images (see tutorial Case 1). 2. Windowing First of all, we have to adjust the contrast of the images displayed in the different views. Contrast enhancement is a very good tool for selecting parts with different intensities, e.g. bone vs. brain tumor. This action can be performed at any time. You can change the contrast in the corresponding tab of the Project management. The contrast tab shows the histogram of the project with a line representing the window. The gray values or Hounsfield units below the start point of the line will be displayed in black. All gray values above the end point of the line will be displayed in white. The gray values in between the window will be mapped on a shade of gray. You can change the window size by clicking your left mouse on one of the points and dragging it to its new location. To move the window select the line and drag it to its new position. You can also choose one of the predefined windows by selecting the appropriate scale from the menu on the bottom of the tab. The following steps will describe the necessary actions to achieve a nice segmentation mask. A segmentation mask is a collection of pixels of interest that constitute an object you wish to work on. One can create several - dependent or independent - masks, each displayed with their own identifying color. Usually several masks will be needed to obtain a final segmentation object that contains the information that is needed. 3. Thresholding Thresholding means that the segmentation object (visualized by a colored mask) will contain only those pixels of the image with a value higher than or equal to the threshold value. Sometimes an upper and lower threshold is needed; the segmentation mask contains all pixels between these two values. For example: 13

16 Table Of Contents A low threshold value makes it possible to select the Soft tissue of the scanned patient. With a high threshold, only the very dense parts remain selected. Using both an upper and a lower threshold is needed when the nerve channel needs to be selected. Defining a good threshold value also depends on the purpose of the model. If you just want a nice looking model, a lower threshold value is recommended since it will result in a model with fewer holes. On the other hand, when the model serves for modeling prostheses a higher threshold value is preferred. Click the Threshold button. To change the threshold value, press the left mouse button on a slider in the Threshold Toolbar and move the slider by moving the mouse (while still holding the left mouse button). Some tips for selecting an adequate threshold value: Look at different images. You can change images of any view by: using the arrow keys, the page up and page down keys using the slider on the right in the window border moving the slice indicators Click the Profile button. In the axial view draw a line over the bone as shown below. To draw this line, click the left mouse button in the soft tissue to indicate the starting point, move the mouse over the bone click. Along this line an intensity profile is generated. The straight horizontal lines represent your current threshold value. Click on Start Thresholding and drag the lower straightline up/down to set a good threshold. If you want a good visualization model, select a threshold slightly above the intensity plateau of the soft tissue. If your model will serve for modeling prostheses, place the line between the soft tissue plateau and the top value of the bone. If a proper threshold is set, click on End Thresholding to save the current value. 14

17 Mimics Tutorial Zoom in on a part you re interested in. First, from the pull-down menu next to the zoom button, select Box. Click the Zoom-button : the mouse is displayed as a loupe. Click the left mouse button on the image and drag for creating a zoom rectangle, release for zooming. To return to the whole image, click the Unzoom-button. A good threshold value for Mimi is about 270 (Hounsfield scale). The threshold value is displayed in the Min. box of the Threshold toolbar. To end thresholding, click the Apply button. After the thresholding operation a green mask will be created. In a project you can have different masks but you can use the segmentation tools only on the active mask. To choose the active mask, select it in the mask tab in the project management. In case the project management isn t active, select the project management button in the main toolbar. You can also hide any mask by clicking on the glasses of the corresponding color. 4. Region growing The region growing tool makes it possible to split the segmentation created by thresholding into several objects and to remove floating pixels. Click the Region growing button or press Ctrl + R. The mouse is now cross-shaped and the Region Growing window is on the screen. 15

18 Table Of Contents Select the Source (= Green) and Target mask (= New Mask). Click the left mouse button on one point in the green area of the object of interest (which is a part of the current segmentation object, i.e. part of the skull). The program starts to calculate the new segmentation, all points in the current segmentation object that are connected to the marked point will be used to form a new mask. The new segmentation is colored yellow. Click the Close button to close the Region growing window. To make this new mask active, select "Yellow" in the Visualization toolbar. Clicking on the green glasses will hide the green mask. Clicking the button again will make the green mask visible. Check the mask on different images. When we check the images, we see that everything looks fine. It s time to build a 3D representation. Note: Thresholding needs to be done before region growing, since all previous work is lost after changing the threshold value. 5. Creating a 3D representation In the mask tab you see all created masks listed with their respective threshold. The names of these masks are Green and Yellow. Selecting one mask will make it active. Now, you still know that the Yellow mask contains the skull, but after a month, when you reload a project, it might be difficult to know in which mask your end result was stored. Therefore, it may be interesting to rename the mask (in Project Management, Masks tab). Click on the name Yellow so that it becomes editable; replace Yellow with a more telling name like skull. Click on the Calculate 3D button. 16

19 Mimics Tutorial The "Calculate 3D Models" Dialog box is displayed. Here you can select from which masks you want to calculate the 3D model. To select multiple masks hold the Ctrl key while selecting the other masks. In this case select skull and press the Calculate button to generate a 3D object. You can set the visualization quality of your model. This is only the visualization on the screen; this parameter doesn t need to have any impact on the model that you will actually build on an RP machine!!! Of course, the lower the quality, the less time the program needs to calculate the 3D image and the less memory is needed to load the 3D image afterwards. 6. Displaying a 3D representation In the vertical 3D toolbar on the right, you can set the visibility of the different calculated 3Ds. This can also be done in the Project Management's 3D Objects Tab, by clicking on the glasses. Once the 3D image is loaded, different operations are available: rotate the model with the button on the right of the 3D window or moving the mouse pressing the right button select different standard views, like Top, Front, Bottom, by clicking on the button on the right of the window zoom with the buttons or Pan with the change the color of your model and background by clicking the right mouse button and selecting the option Color The model can also be displayed transparent. To do so, push the Toggle Transparency button. You can switch between different degrees of transparency (high-medium-low-opaque) by clicking the square button in the transparency column of the 3D objects tab. 17

20 Table Of Contents To change the background color, go to View > 3D Background Color and select the color you prefer. 7. STL+ procedures The intermediate file between Mimics and STL+ can be one of the following:.3dd file Masks 3D Objects You can create a skull.3dd file by clicking the Export 3dd button in the Project Management s Masks Tab or with the option Export > 3dd in the main toolbar. After clicking the Save button the.3dd files will be placed in the MedData folder. This step is not always necessary. Calculation of the machine files can be done directly on the masks or on 3D objects. Click on the STL+ button in the Masks Tab of the project Management. Press the STL+ button and a window will pop up on the screen with 3 different tabs for each option. Choose the Masks tab, select the mask called skull and click the Add button. Choosing the 3D tab would have enabled you to select a 3D object. Please note that multiple 3Ds or masks can be selected and added to the list but it is not possible to add both masks and 3Ds. If you're interested in creating files for Rapid Prototyping or exporting an STL or VRML file, please continue this tutorial. After selecting the mask or the.3dd file and pressing the Add button, the file appears in the output area. If you wish, you can rename the output file to skull (in the same way as you would in Windows Explorer). Select the output format. Depending on the type of output file format, there are different possible formats, like STL or VRML. 18

21 Mimics Tutorial 7.1 Generating a STL file Click the Next button: the Conversion to STL Dialog box is displayed. You can use the parameters as they are displayed in the screenshot. Further details about these parameters can be found in the manual. By clicking on the help button you will immediately be taken to the respective chapter. To generate an STL file, fill in the appropriate values like in the dialog box and click the Finish button. The calculation starts and an STL file is generated. 19

22 Table Of Contents 8. RP Slice procedures 8.1 RP Slice procedures Within the RP slice dialog you are able to generate a contour file from a mask or a 3dd and you can also generate a support file from a contour file. 8.2 Generating a contour file Go to Project Management, Masks tab and choose from the action list the RP Slice button. Choose the mask called skull from the list in the Masks tab of the RP Slice window that just opened and press the Add button, the mask will appear in the area below. Select the SLI Output format. Click the Next button, the Conversion to RP format Dialog Box is displayed. You can use the following parameters in the RP Slice Parameter dialog box. 20

23 Mimics Tutorial Click the Next button to proceed; the Calculation Parameters dialog box is displayed. Fill in the values as displayed below. Further details about these parameters can be found in the RP slice part of the manual. Click the Finish button; the calculation starts and an SLI file is generated. For calculating the support structures, please continue this tutorial. 8.3 Generating supports For building the object with Stereolithography, a support is generated directly from the slice file with RP Slice module. Go to the RP Slice window, Contour files tab and select.sli file option in the Input format field. Select the file you created in the previous section and press the Add button. 21

24 Table Of Contents When one contour file is selected, the Next button in the RP slice Mask/3dd/contour file selection window opens the window displayed below. 22

25 Mimics Tutorial Note: It is also possible to generate slice files for Stratasys machines. Instructions on how to use these files in Quickslice are also provided (read the STL+ Reference Guide). The program defaults to full height, so that the whole model is supported. This isn t always necessary. Check the slices from bottom to top and search for new islands. To prevent that these islands start floating during the building process, they certainly need support. In the case of "Mimi", a support till layer height is sufficient (depending on the resin used). Press the Finish button to start the support generation; an SLI file is created. You now have a model and support file, good luck with the building of the model!! 23

26 Table Of Contents 9. View of end result 24

27 Chapter 3: Simon The Simon case is an example of a dental segmentation. The mandible of the patient was partially edentulous and needed a prosthesis. First, a scan prosthesis was made that resembled the new teeth to be implanted. The patient had this prosthesis at the correct position in his mouth during the CT scan. Because scan prostheses are made out of barium sulfate, an opaque material, they are clearly visible in a CT image. The result is that you see both the bone and the prosthesis in one image, well positioned against each other. Such a procedure with a scan prosthesis gives better esthetic results and the surgeon is able to make a better planning. The images in the Simon project are CT scans of the jaw together with the scan prostheses. It will be your job to do the segmentation of the mandible and the prosthesis. The topics that will be discussed are: Opening the Project Preparation of the data o o o o o o o Windowing Thresholding Region growing Editing Artifacts Multiple particles Scan prosthesis Boolean Operations View of the end result 1. Opening the project In the File menu, select Open (Ctrl+O). Double click the Simon.mcs file. 25

28 Table Of Contents 2. Preparation of the data 2.1 Windowing For correct windowing see the windowing procedures in "Mimi" (Case 2). 2.2 Thresholding Go to an axial image where the mandible (without the teeth) is visible (for example, at position ). Press the Profile line button and draw a line over the bone. The figure below shows a profile line and the corresponding profile dialog box. Press Start thresholding and drag the threshold line to a value of about 538 (Hounsfield scale). End the thresholding and save your settings. Close the dialog box. 26

29 Mimics Tutorial Profile line over the bone (upper image) and the corresponding profile dialog box 2.3 Region growing Press the Region Growing button and click on the bone of the skull to start the region growing. The skull is now added to a new mask. Click on the Project Management icon. In the Masks tab, double click the name of the mask and change it to skull. Make the previous mask invisible (make sure the skull mask is active before making the first mask invisible). 2.4 Editing - Thresholding Separating maxilla and mandible To separate the mandible from the maxilla, we have to disconnect them manually. Therefore we erase a layer from the active mask somewhere between the mandible and the maxilla. Then we perform a region growing on the mandible. The result is that both mandible and maxilla will be in a different mask and thus separated. Look at the sagittal image and place the horizontal indicator between the maxilla and the mandible. Note that it will not be possible to separate them correctly in every image, so we have to find the best possible position. 27

30 Table Of Contents In the corresponding axial image all pixels have to be removed from the active mask. The position of the axial image corresponding to the position of the horizontal indicator in the figure above, is Go to this image and press the Edit masks button. Select the Erase mode, choose a big square as type of cursor and remove all pixels from the active mask. Make sure you don t forget any! Go to a lower image in the data set and do a region growing of the mandible (do not activate the Leave Original Mask option). Now you have two masks, one for the mandible and another for the maxilla. Note: In the region growing toolbar, if you activate the Leave Original Mask option, the pixels selected with region growing will be put into a new mask, but they will also remain in the original mask. If the result of the region growing is not satisfying, you still have the complete original mask and you can start over. If this option is not activated, the pixels selected during region growing are removed from the original mask. In this case you can t do the region growing again from the same original mask. Change in the Project Management the name of the two masks to mandible and maxilla respectively. In figure below, these two masks are shown and the red line in between indicates the layer that was removed from the active mask. But be careful! Because it was not possible to perform the separation 100% correct, we will still have to edit the images and make sure that all the pixels that belong to the mandible are really in the mandible mask. 28

31 Mimics Tutorial Scroll through the coronal images and check if every pixel that belongs to the mandible is in the proper mask. Do you notice at position that some pixels (at the left side in the image) from the maxilla are wrongly put in the mask of the mandible? Move both indicators until their point of intersection indicates the wrong pixels (figure above). It concerns two layers of pixels, belonging to a tooth of the maxilla. In the two corresponding axial images (position -6,50 and - 5,50), erase the tooth from the mask of the mandible. You cannot be mistaken, because that tooth is also indicated with the point of intersection of the indicators (figure below). If the two layers of pixels are shown in grey values in the coronal image, you can be sure you erased the whole tooth from the mandible mask. If not, move the indicators again in the coronal image so their intersection points to the wrongly colored pixels. In the axial image, remove the pixels that are indicated by the indicators from the active mask. 29

32 Table Of Contents Note: you can still access the 1-click navigation function by pressing the SHIFT button while you are editing. You can then click with your left mouse button on the point you want to navigate to. Axial images (position: left -5,50, right -6,50): the indicators point out the tooth that does not belong to the mandible mask. In the sagittal image at position (or the coronal image at position 43.25) another collection of badly masked pixels is visible. But now it s the opposite situation! Three layers of pixels that belong to the mandible are not in the mandible mask. Two layers belong to the maxilla mask and the other layer is the one we erased in the beginning to make the disconnection. Again, mark these pixels with the indicators as it is done in the figure below. In the corresponding axial images (at positions and and -2.50) the pixels (of a tooth) should be added to the mandible mask. We will make use of a local threshold to do this. To make this threshold clear, a short intermezzo is inserted below. 30

33 Mimics Tutorial Indicators point to pixels that should belong to the mandible mask (sagittal view). Local threshold: In the obturator case it is mentioned that there are three modes to choose from in the Edit toolbar, i.e. draw, erase and threshold. The threshold mode (Ctrl + T) is used to set a local threshold. This means that if you apply a local threshold in a particular area of one image, this threshold doesn t apply to the other images in the project. Remark that the threshold we ve set in the beginning of this case was global and it applied to every image in the dataset. When you activate this mode, the box with the two default threshold values is shown on your screen. To set a different local threshold, press one of the two arrow buttons and double click on a threshold value. After you changed the value, press Enter. When you move the square over the image while pressing the left mouse button, every pixel that comes to lie within the square and has a threshold in the threshold range you just set, will be added to the active mask. On the other hand, all the pixels that already belonged to the active mask and that don t have a grey value within the range will be removed from the mask. The local threshold range For the moment we don t have to change the threshold values, but it will be used later on in this case to remove artifacts out of the image. 31

34 Table Of Contents Maybe you now wonder why we will add the pixels of the teeth that belong to the mandible with this local threshold method and not with the draw mode we will use in the obturator case. With the draw mode, can t you also add pixels to a mask? Yes, that s true, but there is a difference! With the draw mode you add every pixel you touch with your cursor. With the threshold mode you do the same, but there is one more condition before they are really added: their HU values must lie in the range shown in the box (figure 3-7). In this case, it s much safer to add pixels by taking into account their grey values. Our segmentation will be more accurate. Press Ctrl + T. The Edit toolbar shows up and the threshold mode is already selected. Choose a circle as type of cursor and make it more or less the same size as a tooth. Make sure that the mandible mask is the active mask. Press the left mouse button and go over the tooth with your cursor. Make sure you got the tooth completely. You can check this very easily by looking at the sagittal or coronal image: if the wrongly masked layers (figure 3-6) now have the color of the mandible mask it s alright, otherwise you ve forgotten some pixels. Suppose you added too much pixels, just press E (or select the Erase mode with your mouse) and erase them. If you repeat the thresholding in the necessary axial images (see before to know their positions) you should become a sagittal image like in the figure below. Now we can say that the whole mandible is in the mandible mask Artifacts Sagittal image after local thresholding The images still don t look nice, because of all the artifacts. We are going to get rid of them by again performing a local threshold, but not the default one like we just used to add the pixels. 32

35 Mimics Tutorial To enter the Edit mode, press Ctrl + T. The threshold mode is already selected. Click on the top arrow of the threshold range box (figure 3-7) and double click the threshold 1 value. Change this value to 3000 (if you are working in Hounsfield Units) and press Enter. Because the Hounsfield Units of the artifacts are lower than the ones of the teeth. Go with your cursor over the artifacts and notice that they disappear. Why do we use this high local threshold? Because the HU values of the artifacts are lower than the ones of the teeth. So by setting a very high threshold the artifacts will be removed from the mask because their grey values are not in the range. Moreover, if you accidentally go with your cursor over the teeth, their pixels will remain in the mask, except for the edges (their HU are lower). If you removed the edges from the mask, don t panic. Set the threshold range back to the default one by clicking once on the lowest arrow and move your cursor over the tooth again to restore the edges. So, this is the way you should work. Scroll through the axial images and remove all the artifacts from the mask of the mandible. The artifacts in the left image are removed with a local threshold. The right image shows the result Multiple particles Let s calculate the 3D image of the mandible. Press the Calculate 3D button and select the mandible mask to be calculated (choose low quality). You get the message that the mask consists out of multiple parts. Answer with Yes. 33

36 Table Of Contents Visualize the 3D by pressing the 3D button. Rotate the model and remark that there are little particles floating around the mandible. That caused the message you got about the multiple parts. The particles are due to the editing you ve done to remove the artifacts. To avoid this you have to do a region growing before calculating the 3D. Press the 3D view button again to get back the sagittal image. Press the Region growing button and click into the mandible. Change the name of this new mask to Total mandible. Now calculate and visualize the 3D model of the final mandible. You can delete the first 3D (with the particles) listed in the 3D tab of the Project Management Scan prosthesis Can you distinguish between the natural teeth and the scan prostheses in the 3D model of the mandible? It s quite simple; the natural teeth are connected to the bone, while the scan prostheses are not. There are 3 teeth of the scan prostheses at the patient s left side and one at his right side. In the figure below, the scan prosthesis (axial view) is marked with rectangles. Axial image indicating the prosthesis in the boxes. We would like to have the mandible without the prosthesis and the prosthesis itself into two different masks. There are two ways to achieve this. The first one is to proceed with the segmentation of the final mandible and to remove the prosthesis from the active mask. The second option is to perform a segmentation of the prosthesis. We opt for the latter. We will do a region growing of the prosthesis twice, once at either side. But, we first have to make sure that the prosthesis is completely disconnected from the natural teeth. The intention is to remove (from the final mandible mask) the pixels surrounding the prosthesis and the pixels connected to the prosthesis. The goal is to get the prosthesis nicely isolated in every image. Keep the following advice into account: remove enough pixels in the surrounding of the prosthesis, because sometimes in 2D it looks like there is no connection, but there is still one in 3D. So a 3D model can be very tricky! 34

37 Mimics Tutorial Project Management Masks tab Make the mask of the final mandible active and press the Duplicate button in the Masks tab of the Project Management window. This way a backup mask is created that we can use to do the segmentation of the prosthesis, while the original Final mandible mask is left unchanged. The original one will be used later on to perform Boolean operations. Proceed with this backup mask (if you don t like the color, press the Color button in the masks tab and choose the color you like). Scroll through the axial images and remove (enough!) pixels surrounding the prosthesis from the active mask. In the figure below it is shown for the axial image at position - 11,50. If you think you disconnected the prosthesis completely, press the Region Growing button. Make sure your target mask is a new mask (if not, select new mask from the drop down list) and that you activate the Leave Original Mask option. This last option is very important! The prosthesis is disconnected in this layer 35

38 Table Of Contents Click on the left or the right prosthesis. If you disconnected the prosthesis entirely, only the prosthesis should be shown in the color of the target mask. If this is not the case, make the previous mask active again, delete the last mask in the list (generated for the region growing) and remove more surrounding pixels from the backup mask. Also in the layers where you don t see the prosthesis it can be useful to remove some pixels belonging to the teeth next to the prosthesis. repeat these actions for the prosthesis at the other side. Give the masks of both prostheses proper names. 2.5 Boolean Operations Let s examine what we ve obtained so far: the final mandible (with prosthesis), the left prosthesis and the right prosthesis in three different masks. That s nice, but we said earlier that we would like to have the mandible without prosthesis. We can achieve this with some Boolean operations we can achieve this. Press the Boolean operations button. Let's use the following calculation: Mandible without prosthesis = total mandible left prosthesis right prosthesis Follow the steps below: Mask A: final mandible Operation: minus Mask B: left prosthesis Result: new mask (called mask C for reference) After these options are set, press the Apply button. Mask A: mask C (obtained in the first step) Operation: minus Mask B: right prosthesis Result: new mask After these options are set, press the Apply button. Press the Close button. The last mask (the one that should be active now) contains the pixels of the mandible without the prosthesis. Calculate and view the 3D of this mask. Show also the left and right prosthesis. The other 3Ds can be set invisible. You should have a model that looks like this one. 36

39 Mimics Tutorial 3. View of end result 37

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41 Chapter 4: Hip In the fourth tutorial we will discuss some of the possibilities of the MedCAD module. To finish this tutorial you will have to have a license for the MedCAD module. The topics that will be discussed are: Opening the Project Preparation of the data o o Thresholding Region growing Calculation of the Polylines Patching of the contours Creation of MedCAD objects Visualization possibilities 1. Opening the project The objective for this part is the creation of a file ready to use in all CADsystems supporting the IGES-interface. The part of the "Hip" we ll focus on is the right femur of the patient (left in the images). In this IGES-file a basic reference system calculated on the data as well as a partial modeling of the outer contours using freeform surfaces will be present. It is strongly advised to first follow the tutorial of Case 2 to obtain the necessary skills for segmentation and image processing. In the File menu, select Open (Ctrl+O). The Open dialog box shows all projects in the working directory. Double click the hip.mcs file (Mimics project file). 2. Preparation of the data 2.1 Thresholding A good minimum threshold value for this case is 1235 (Grey Values) or 211 (Hounsfield values). Set this threshold in your base mask and apply it. The procedure is explained in more detail in Case 2. 39

42 Table Of Contents 2.2 Region growing We want to make a model of the right femur (left in the image set). Therefore use the following steps: Click the Region Grow button or press Ctrl + R. Set the Source to Green (if this is your base mask) and Target to New Mask. Check the Multiple layer box. Click the left mouse button on one point of the right femur (left on the images). The right femur has now been grown into a new mask (Normally if you have started fresh the femur will be in the yellow mask now). To calculate your 3D, go to Project Management, Masks tab, select the yellow mask and press the Calculate 3D button. The yellow mask will be automatically selected in the Calculate 3D window, but you need to set the quality to high and press the Calculate button. You can find more details about this in Case Calculation of the Polylines Go to the Project Management. Project Management - Masks tab Select the yellow mask and click on the action button, select the Calc Polyline option from the action list. The Create Polylines dialog box appears with the Yellow mask already checked; click OK. The borders of your yellow mask will be calculated and displayed as a polyline in both 2D and 3D images. 40

43 Mimics Tutorial 3D view of the polylines You can also calculate polylines by clicking the segmentation toolbar. button in the 4. Patching of contours Since we are only interested in the outer contours, we need to select these out and grow them to a new set of polylines. Go to layer -523 and zoom in on the right femur in the 2D image (xy plane). Click the Polyline Growing button in the MedCAD toolbar. Set all parameters as displayed in the image below: i.e. the set to start from, the set that will contain the grown polylines,... In order to select a polyline, you need to draw a rectangle over it or simply click on its contour. Hold the left mouse button down, drag it and then release the left mouse button. 41

44 Table Of Contents The growing of the polylines stopped at layer -513 because of a small extension on the bone This needs to be removed in layers 513 and Next the polylines need to be updated and then we can proceed with the polyline growing: Click the Edit masks button and go to the erase mode or press Ctrl + E Make sure that the Yellow mask is Active Erase the extension on the bone Press the Ctrl + U key or the Update Polylines button in the Edit toolbar Repeat this for the following images. Scroll back to image -513 and click the Polyline Growing button. Set "selection 2" as the target polyline and use 96 % as matching parameter. Select the polyline. Scroll to image 485 (figure below). Image 485 of the Hip 42

45 Mimics Tutorial At this slice you see a cavity in the contour. If you want to restore this with editing, keep in mind that it will be the yellow contours that will be updated, so we need to remove the pink polyline first. Do a Polyline Growing from Selection 1 to a New Set ; be sure to turn Auto Multi-Select off. You can delete this set by selecting it in the Project management and then pressing the Delete button. Lose the cavity by drawing in the mask and updating the polyline (Ctrl + U). Similar editing and updating of the polylines needs to be done on slices: till -479, -475, -471 (on the femur head). Don't forget to update for every image. When all corrections have been made, the polyline growing can continue. Go back to layer -485 and perform the Polyline Growing (from Set 1 to Selection 2, matching parameter 95 %, Auto Multi-Select on) When all editing was performed properly, all layers until -477 are now stored in Selection 2. The femur head and the greater trochanter will be grown into new selection sets. The end result should look like the figure below. Polyline sets 5. Creation of MedCAD objects On the great trochanter and on the lower part of the femur we will fit a Free Form Surface, on the femur head, we will fit a sphere. 43

46 Table Of Contents In the Project Management on the Polylines tab, you will find a button Fit Surface. Choose Selection 2 and press the Fit Surface button. The following dialog box will appear. Surface Fit Parameters You can accept these default values and a Free Form Surface will be fitted on Selection 2. Note: Some caution in increasing the number of control points is advised. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave. So, if the number of points is too high, the fit on the polyline will become worse. Repeat this set on Selection 4. The Free Form Surfaces are visible in 3D as a shaded surface and in 2D you will see a cross-section on every layer of this Free Form Surface. To fit a Sphere on Selection 3, go to the MedCAD menu and select Sphere > Fit on Polylines. Choose the correct polyline set. The result of all these fittings should look like following figures: 44

47 Mimics Tutorial Objects fitted on the Polyline sets Imported STL files 6. Visualization possibilities When a prosthesis is designed, the STL file can be loaded in Mimics. One can rotate and move this prosthesis to obtain the best fit of the prosthesis onto the femur and check the design related to the bone structures. You can import an STL file in the Project Management from STLs tab. Click the Load... button. Browse to the MedData folder and select the prosthesis.stl. The STL file will be visible both in 2D (as cross-sections) and in 3D. To adjust the position of the STL file, click the Move button to move the STL file or the Rotate button to rotate it. Both actions can be performed in 2D as well as in 3D. 45

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49 Chapter 5: Obturator In the previous cases we have segmented bone structures, whereas in this project we are going to make a soft tissue model. An interesting application is the modeling of the soft tissue around the cavity of the mouth. Such a model can be used as a mold for obturator prostheses. In the case study following this introduction we will do just that. How are we going to model this soft tissue? Since we are only interested in the area around the cavity, we need to limit the model to the region of interest. By erasing one layer from the active mask in every direction, the cavity and the soft tissue around it will be separated from the rest of the image. This way the region of interest is captured in a 3D box delimited by the removed layers. Next we perform a region growing that starts in the region of interest. Because this region is separated from the active mask, only this area will be put into a new mask after the region growing is done. From the new mask a 3D model can be calculated which will contain just the cavity of the mouth and the soft tissue surrounding it. The topics that will be discussed in this tutorial are: Case Study Preparation of the data o o o Editing Windowing Orientation Thresholding Region growing View of the end result 1. Case study Obturator prosthesis for oncologic patients Case presented by Dr. L.L. Visch from Daniel den Hoed Kliniek Rotterdam. The first picture shows the cavity in the mouth of the patient after resection of a tumor. In order to protect the tissue weakened by irradiation and to be able to breathe and eat normally, this hole needs to be filled by an implant. 47

50 Table Of Contents A CT-scan of the patient was made. The soft tissue around the cavity, clearly visible on the scans, was modeled. This model served as a direct mold for the implant. The implant, called an obturator prosthesis, was cast from the mold in a biocompatible silicone. 48

51 Mimics Tutorial Absolutely no surgery was needed to implant the obturator prosthesis. As the silicone prosthesis is plastic deformable, it can be implanted very easily. The prosthesis fits the cavity much better than ever could have been achieved by using conventional impression techniques. These traditional techniques produce a master of the obturator prosthesis by making an impression of the cavity in a deformable plastic material. The prostheses cast from such masters are always less accurate because of the presence of undercuts (the impression technique is not sensitive to local internal broadening of the cavity) and can severely damage the sensitive and vulnerable surrounding tissue. The soft prosthesis is fixed by means of magnets on a hard dental implant. This makes it possible to take it out for inspection and to replace it afterwards. 2. Preparation of the data 2.1 Preparation of the data In the File menu, select Open (ctrl+o) or click the button the obturator.mcs project.. Double click 2.2 Windowing For correct windowing see the windowing procedures in "Mimi" (Case 2). 2.3 Orientation When the project is loaded, a Change Orientation window pops up. 49

52 Table Of Contents In the axial image you see the orientation strings L and R, which stand for Left and Right respectively. In the coronal and sagittal image several Xs are displayed instead of the orientation strings. Move the mouse cursor to the top X in the sagittal or coronal image. The cursor is changed to a hand and when you right-click, a menu appears with all possible orientation strings. Select Top. Remark that all other orientation strings are completed automatically. Do the same to set the Anterior-Posterior orientation parameter looking at the image displayed. You can always change your orientation parameters, going to File > Change Orientation. 2.4 Thresholding A reliable way to define an appropriate threshold is to make use of a profile line (see also Case 2). Press the Profile line button the axial image over the cavity. and draw a line in 50

53 Mimics Tutorial Profile line over the cavity of the mouth See the figure above (axial image on position 374) to have an idea where to place the profile line. You get a profile like shown in the image below. You can clearly see the transition from the soft tissue to the cavity. Press the Start thresholding button. To visualize all the soft tissue in the mask, drag the lowest threshold line to the value 444 (Hounsfield scale). Press again the End thresholding button and answer yes to the question whether you want to save the threshold value or not. Close the window. 51

54 Table Of Contents 3. Editing In the axial image, go to position 387,00. Press the Edit masks button. The edit toolbar is displayed on your screen. Your cursor has become a little square. If not, go to Type and select a square from the drop down list. Notice that the length and the width of the square are displayed and can also be altered. The easiest way to change the size is to press the control key and your left mouse button simultaneously and to move to the right/left to make the square bigger/smaller. The three modes available are listed below. To make a mode active, just click in the little circle on the left of the mode or press the first letter of the desired mode. When the edit mode is not yet selected and you use the shortcuts between parentheses below, the edit toolbar appears and the associated mode is activated. Draw (Ctrl + D): Every pixel that lies within the shape of your cursor, while pressing the left mouse button, will get the color of your active mask. In other words, you add pixels to the active mask by going over the pixels with the square. 52

55 Mimics Tutorial Erase (Ctrl + E): This mode is the opposite of the draw mode. You remove all the pixels from the active mask by moving the square (keeping the left mouse button pressed) over the pixels in the image. Threshold (Ctrl + T): This mode is used to set a local threshold. This means that if you apply a local threshold in a particular area of one image, this threshold doesn t apply to other images in the project. Remark that the threshold we ve set in the beginning of this case was global and it applied to every image in the dataset. When you activate this mode, a box with the two default threshold values is displayed on your screen. To set a local threshold, press one of the two arrow buttons and double click on a threshold value. After you have changed the value, press Enter. When moving the square over the image while pressing the left mouse button, every pixel that comes to lie within the square and has a threshold within the threshold range you set, will be added to the active mask. On the other hand, all the pixels that were already part of the active mask and that don t have a grey value within the range will be removed from that mask. For the current case we are only going to use the draw and the erase mode. In the Simon case we already illustrated the threshold mode. Working on the axial image in position 387 activate the Erase mode (Ctrl + E) and set a very large square (for example, 200 by 200). Press your left mouse button and wipe off all the color in the image. Be sure not to forget any pixels! Close the Edit toolbar. Notice in the sagittal image that one layer is shown in grey values. In the figure below, the sagittal image is displayed and the arrow points to the layer that has been removed from the active mask (the slice indicator is moved down to see this). 53

56 Table Of Contents To see the result of erasing the mask in one layer, we will now perform a region growing. Select the axial image at a position lower than 387,00, (= the position of the image we removed from the active mask). Press the Region Growing button, a window will be displayed on the screen. Check both the Multiple Layer and Leave Original Mask checkboxes and click on an arbitrary position in the active mask. You see that all the images at a position lower than 387,00 are put into a new mask (yellow mask in figure below). Close the region growing toolbar. 54

57 Mimics Tutorial Why are the images above this position not included into the new mask? As you already know, a region growing looks for pixels that are connected to each other and puts them into a new mask. But, because we have disconnected the lower images from the higher ones, we have limited the area of the region growing. This will be the trick we will use to get our region of interest into a separate mask. How will we proceed? In the same way as above, we are going to erase a complete layer from the active mask on every side so that our region of interest is completely surrounded by these removed slices. After we perform a region growing within that region, we should have the oral cavity and the surrounding tissue in one mask, like we wanted. Activate the axial image. Go to position 362,00 and press Ctrl +E (or press the Edit masks button and select the erase mode). Make a big square and erase all the pixels from the active mask. Take a look at the sagittal image. Two horizontal lines are shown in grey values. The top and the bottom of our box are now defined. To set the left and right boundaries of the box, you have to remove two layers from the mask in the sagittal image. Try to visualize the situation and make sure you understand why we will now operate in the sagittal image. Erase all pixels from the active mask at position 126,49 (left boundary) and 42,05 (right boundary) in the sagittal image. In the axial image two vertical lines in grey values are visible. To close our box, a separation still has to be made on the posterior side. Activate the coronal image and remove all pixels from the active mask at position 76,61. In the axial image the removed layer is visible. Setting a boundary on the anterior side is not necessary. In figure 5-10 you can see the boundaries of the obturator on the yellow mask. 4. Region growing Now that the box is delimited by the layers removed from the active mask, a region growing can be performed to get the obturator into a new mask. Go to an axial image that has a position between 362,00 and 387,00. This is to make sure that the starting pixel for the region growing lies within the region of interest. Press the Region growing button and click in the axial image within the box. 55

58 Table Of Contents Boundaries of the obturator in the axial image. The obturator is now within a new mask. In the figure below you clearly see the obturator within the active (blue) mask from the axial and the sagittal viewpoint. 56

59 Mimics Tutorial Axial and sagittal view of the obturator Because we disconnected the pixels of the obturator from the other pixels in the original mask, the region growing was confined to the region of interest. Press the Calculate 3D button and select the mask of the obturator. Choose custom quality and press the Calculate button. The processing of the 3D model is started. To visualize the 3D image, make the axial image active and press the 3D View button. Note that the model will always be visualized in the sagittal view, unless you select to view it in a fourth pane in Options > Preferences > Visualization > View. On the right of the 3D object you see a toolbar and a button where you can select some predefined viewpoints for your 3D model. If you press the bottom view you should obtain a model as shown in figure You can also enable transparency using the button. 57

60 Table Of Contents 5. View of end result 58

61 Chapter 6: Manual Import In this case we will show you how you can use the manual import function to import any image data you want. The topics that will be discussed in this tutorial are: Importing images Manual Import o o o Parameters Preview the images Convert the images Choosing the right parameters 1. Importing images The goal of this chapter is to teach you how to import images with the Manual Import option and convert them to a Mimics project. Select Import Images from the File menu. An Import Project Wizard will be displayed where you need to point to the "MedData\Import3" directory (STEP 1) 59

62 Table Of Contents There are 3 ways to import images, depending on their file format: automatic, semi-automatic and manual import. Only the manual import will be explained in detail, because the other ways are more straightforward to use and are mentioned already in the tutorial Case 2. Note: When you press the Next button, all the project files listed will be converted. Select only the files you want to convert and leave the others unselected. 2. Manual import 2.1 Manual import In the first step of the wizard, browse to the following path: \MedData\convert\. The images will be selected automatically. Select the Manual Import button and press Next. A new window is displayed on your screen. The most important parameters are explained in the next paragraph. 60

63 Mimics Tutorial 2.2 Parameters File header size The file header size is calculated automatically, based on the file size, the resolution of the images and the pixel type. Typically a file contains both a file header and the image itself (in some rare cases also a footer is present). The file header can contain information about pixel size, patient data, The image is a matrix of pixels. The horizontal (or vertical) image size is equal to the number of pixels in that direction. 61

64 Table Of Contents Structure of a file Common sizes of images are: 256 * * * 1024 The number of bytes per pixel depends on the type of the pixel. Some examples of pixel types and their respective sizes (note that these types can be either signed or unsigned, however, this does not affect their size): Byte: 1 byte Short: 2 bytes Long: 4 bytes Float: 4 bytes Image size = horizontal image size * vertical image size * number of bytes per pixel In this example, the images have a resolution of 256*256. If you fill these values in, you will see that Mimics will set the file header size to 8432 bytes Exam information Fill in an appropriate name for the patient name. This will be the name that is used for your project. 62

65 Mimics Tutorial Image information In the Image Information frame you see that the value for the image size is still 512*512. Correct the size to 256 * 256 pixels. The default values for the other parameters are correct in this case Pixel properties Select Signed Short for the parameter Type and Low Byte First for the parameter Byte Swapping. 2.3 Preview the images Press the Show Preview button and take a look at the images to check whether the parameters we filled in were correct. On the left side, the first of the 8 images is displayed. Scroll through the images by moving the arrow on the right (or use your mouse wheel if you have one). For each image a histogram is displayed that gives you information about the range of grey values that are present in the image and their respective quantity. If you want to know the amount of all the different grey values in the entire dataset (and not just in one image), you have to press the Sample button on the right. Notice that the title of the middle frame has changed to Sampled. What if you have a very large dataset? Don t worry, you can restrict the amount of images that is used for this calculation. For example, fill in the number 2 for the interval. Now only 4 images are taken into account, namely the first, the third, the fifth and the seventh image. Press the OK button to close this window. 2.4 Choosing the right parameters Let s experiment a little bit with the different parameters. The examples will help you fill in the right parameters when the image does not look like you expected it to. 63

66 Table Of Contents File header size: Set the file header size back to zero. Select the Show Preview button. Notice that all the pixels are shifted. Fill in the correct value and click the Update button to adjust the preview. Pixel Type: Select Unsigned Short for the pixel type and preview the images. Remark the loss of information due to the restriction to positive grey values. Select the correct type and click the Update button to adjust the preview. Byte Swapping: Choose High byte first for the byte swapping and preview the images. You can see that there are local distortions all over the image, because the data is read in the wrong order. Fill in the correct value and click the Update button to adjust the preview. Influence of the file header size Influence of the pixel type (signed/unsigned) 64

67 Mimics Tutorial Influence of the byte swapping (high first/low first) 3. Convert the images If the images look good in the preview, click the OK button in the Manual Conversion Options window. In the wizard window you should see the name of the patient and some other information about the data. Select the project you want to convert and check the box. Press the Open button, the project will be saved in the default folder (usually MedData). A Mimics project is created from the data and it will be opened automatically showing you the Change Orientation window. 65

68 Table Of Contents Chapter 7: Simulation Tutorial In the Simulation Tutorial we will explain some of the functions that are available in the Simulation module. We will start with a dataset of a skull with a hole in it and explain how to do the segmentation, how to calculate the 3D, how to cut, split and reposition a custom implant. The Simulation module has to be licensed to be able to conclude this tutorial. The topics that will be discussed in this tutorial are: Opening the Project Windowing Thresholding Region Growing Calculating a 3D Cutting Splitting Mirroring Repositioning 1. Opening the project In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Skull_with_hole.mcs file. 2. Windowing For correct windowing see the windowing procedures in "Mimi" (Case 2). 66

69 Mimics Tutorial 3. Thresholding Go to an axial image where the skull is visible (for example, at position 18.94). Press the Profile line button and draw a line over the bone. The figure below shows a profile line and the corresponding profile dialog box. Press Start thresholding and drag the threshold line to a value of about 1250 (Grayvalue scale). End the thresholding and save your settings. Close the dialog box. Profile line over the bone (upper image) and the corresponding profile dialog box 4. Region Growing Now we will use the region growing tool to separate the skull from the artifacts and noise in the images: 67

70 Table Of Contents Click the Region Grow button or press Ctrl + R. Set the Source to Green (if this is your base mask) and Target to New Mask. Check the Multiple layer box. Click the left mouse button on one point of the skull. The skull has now been grown into a new mask. 5. Calculating a 3D Go to the Project Management by clicking its icon Masks tab. and choose the You'll see all created masks listed with their respective threshold. Selecting one mask will make it active and it will appear in the Active Mask field in the visualization toolbar automatically. It is possible to hide/show a mask by clicking on the glasses. 68

71 Mimics Tutorial Click on the Calculate 3D button. The "Calculate 3D Models" Dialog box is displayed. Here you can mark (with a green dot in the column called Selected ) which masks you want to visualize and calculate the 3D by clicking on the Calculate button. Select the "Skull" mask if it is not already selected and click on the Calculate button. 69

72 Table Of Contents 6. Cutting After the calculation of the 3D you will see a 3D representation of the Skull mask. To be able to make a cut that fits well, make the skull transparent by clicking on the button and choose to view the skull from the Right view. Now you can pan and zoom so you can see the hole clearly. If you then zoom and pan, you can clearly view the hole in the skull through the intact side. This way we can easily draw around this hole. To do this, select the Cut with Polyplane tool from the Simulation menu (CMF/Simulation -> Cut -> With Polyplane). You will see following dialog: 70

73 Mimics Tutorial Select the 3D from the skull in the Objects to Cut list. The New button is already enabled so we can immediately start drawing a cutting path. Do this by clicking several times with your left mouse button around the hole like below. To end the drawing, double click with your left mouse button. You can see that a cutting path has been added to the cutting path list. You can now make the 3D opaque again by clicking on the button. You can then rotate the 3D to determine if the cut went through the whole skull or not: 71

74 Table Of Contents As you can see, it would be best if we adjust the depth of the cutting path. You can do this by clicking on the Properties button while the cutting path is selected. This will open the cutting path properties dialog: 72

75 Mimics Tutorial Adjust the Depth of the cutting path from 20.0mm to 30.0mm and enable the Closed checkbox (this will close the cutting path). Click on Preview to view the result. When you are happy with the result, close the Cutting Path Properties by clicking on the OK button. Enable the Keep Originals checkbox (since we want to keep the original 3D) and finish the cut by clicking on the OK button of the Cut with Polyplane tool. You can see in the 3D objects list that a new 3D object was added. 7. Splitting The next step is to split the two cut parts of the newly generated 3D. To do this, go to the CMF/Simulation Menu and choose Split. Select the freeform object, choose to keep all parts and disable the Keep Originals checkbox. You can then click on Preview to preview the split and then on OK to apply the split. 73

76 Table Of Contents As you can see, two different objects were created and have been given a different color. You can make the largest part invisible since we will only need the small part to fix the defect in the skull. 8. Mirroring To mirror the part to the other side of the 3D, we will need a mirror plane. The Mimics simulation module generates a default sagittal plane, but we will have to adjust this plane a bit to make sure it's suitable for this dataset. To do this, go to the Simulation Layout (by pressing F5 or by going to the View menu, choose Layouts and then Simulation Layout). Then make the original skull visible and go to the CMF/Simulation menu and choose Measure and Analyse. 74

77 Mimics Tutorial You can see in the right dialog that you can change the Sagittal Plane. Click on the Change button and adjust the Sagittal plane (by dragging the white points with your left mouse button) in the axial images to make sure the sagittal plane goes through the center of the nose. 75

78 Table Of Contents After this, close the Measure and Analyse tool by going to the Simulation Menu and choosing Measure and Analyse again. Then mirror the part by going to the Simulation Menu, from the advanced Tools select Mirror. Select the correct part and mirror plane and disable the Keep Originals checkbox and click on the OK button to apply the mirroring. 76

79 Mimics Tutorial As you can see, the part is mirrored, but not correctly positioned. We will reposition this part in the next section of the help. 9. Repositioning To reposition the part, got to the CMF/Simulation menu and choose Reposition. This will open following dialog: Select the Mirrored part and start the repositioning. The easiest way to do this, is to first reposition the part with the mouse and then do some finetuning with the parametrical translation and rotation tools. So click on the Move with Mouse button and reposition the part. You can translate the part by dragging the center point with your left mouse button and rotate the part by dragging the corners of the selection box with your left mouse button. Keep in mind that you can also reposition in the 2D views so this makes it a lot easier to get a real nice fit. During repositioning it is also possible to scroll through the axial images to make sure the fit is optimal on all slices. 77

80 Table Of Contents When you are happy with the fit, you can click on the Analyze Motion button to see the final translation and rotation of the part. 78

81 Mimics Tutorial To apply the reposition, click on the OK button. If you have a license for STL+, you can then export the part and the skull to STL files and continue working on the custom implant in your design software. 79

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83 Chapter 8: FEA Tutorial In the FEA Tutorial we will explain the work-flow for making a FEA analysis on a model of the Femur. We will start with a dataset of a Femur and explain how to do the segmentation, how to calculate the 3D, how to remesh the 3D and how to assign materials to the 3D. The FEA and STL+ module have to be licensed to be able to conclude this tutorial. The topics that will be discussed in this tutorial are: Opening the Project Calculating a 3D Remeshing the 3D Creating the volume mesh based on the remeshed 3D Material Assignment Exporting the Volumetric Mesh 1. Opening the project In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Femur.mcs file. 2. Calculating a 3D There is already a Yellow mask available in this dataset that will be used to calculate a 3D object. In the Calculate 3D dialog select the High quality setting and click on calculate. 81

84 Table Of Contents 3. Remeshing the 3D In the next step we will remesh the 3D to make it optimal for FEA purposes. Start the remesher by going to the FEA menu and choose Remesh. You will notice that there are two 3D models, select the yellow 3D model. The FemurShaft model will be used in the non-manifold assembly tutorial. 82

85 Mimics Tutorial The remesher will open with the part already loaded in an inspection scene: There are several Shape parameters available to measure the quality of the triangles. For this example we will use the height/base parameter. This parameter measures the ratio between the height and the base of a triangle and normalizes the value. A perfect equilateral triangle has a quality of 1 and a very bad triangle has a quality of 0. In the quality parameters section select Height/Base(N) from the Shape measure dropdown box. 83

86 Table Of Contents In the Histogram parameter section make sure the current measure is set to Shape measure. This quality histogram shows the amount of triangles that have a certain quality. Then drag the green slider to This is the quality threshold we will use for our project. Below the histogram you can see three values: Value 1 is number of triangles that have a quality below the minimum quality threshold. Since the minimum quality threshold is 0 in our project, there are 0 triangles with a lower quality Value 2 is the number of triangles that have a quality between the minimum and maximum threshold. In this case we have triangles. We will try to increase the quality of all those triangles. Value 3 is the number of triangles that have a higher quality as our quality threshold. In this case For more information about the remesher in general and quality in specific, please have a look in the help pages under the FEA module. 3.1 Remeshing Protocol Below is a description of the remeshing protocol that you can use to remesh the Femur. The values given are those used for the Femur example and will have to be adapted if your part has a different scale (i.e. geometric error, maximum triangle size). The protocol can be divided in three big steps: 1. Reduce the amount of detail 2. Reduce the amount of triangles of your object 3. Improve the quality of the triangles of your object 4. Reduce the amount of triangles while preserving the quality 5. Remove extra shells 84

87 Mimics Tutorial In between these steps measures will be taken to make sure that the object has no intersecting triangles and has no bad edges. STEP A: Because the 3D object will be used for FEA only, you can reduce the amount of detail by applying a smoothing to the 3D object. In the remeshing tab select the smooth icon. Left click on the 3D model and select the 3D model from the context menu: Perform a Lapacian (1 st order) and use the following parameters: Smooth Factor 0.7, 3 iterations and check Use compensation. Step B: The 3D object contains too much triangles for an FE Analysis. To reduce the amount of triangles, go to Fixing -> Reduce (or use the reduction icon in the remeshing toolbar ). Left click on the 3D model to select it and use following parameters Method: normal, Flip threshold angle: 15, Geometrical error: 0.2, iterations 5. 85

88 Table Of Contents STEP C: In this step we will improve the quality of the mesh. As already explained we will use the Height/Base (N) Shape measure. Make sure the Shape measure is put on Height/Base(N) and check if Current measure is set on Shape measure. To improve the quality, go to Remeshing -> Auto Remesh (or use the Auto remesh icon in the remeshing toolbar ) and use the following parameters: quality threshold: 0.4, geometric error: 0.2, control triangle edge length OFF, Number of iteration: 4. Most triangles now reach the desired quality but the edge lengths are still diverse. In order to get a more uniform mesh we can limit the Maximum edge length. To get an idea of the edge lengths present in the mesh select the inspection parameter Smallest edge length or Largest edge length. In the Histogram parameters section put the Current measure to Inspection measure. The histogram will now show the selected inspection measure. In the example below you see the Largest edge length distribution. 86

89 Mimics Tutorial You will notice that most of the triangles have a larger edge length smaller than 5mm. To remove the outliners we will perform the Auto Remesh algorithm again limiting the maximum edge length to 5mm. Go to Remeshing -> Auto Remesh and use the following parameters: quality threshold: 0.4, geometric error: 0.3, 4 iterations, control triangle edge length ON, Maximum edge length: 5. STEP E : The mesh still contains groups of small triangles. These can be removed using the quality preserving reduce triangles. Go to Remeshing -> Quality preserve reduce triangles (or use the Quality preserving triangle reduction icon in the Remeshing toolbar ) and use the following parameters: Quality threshold 0.4, number of iterations 3, Max Geometry error 0.3 mm, Max edge length 5 mm. 87

90 Table Of Contents STEP F: Call the self-intersection test. Go to Fixing -> Mark selfintersecting triangles. No intersections should be found. STEP G: Once you have an adequate surface mesh, you can create your volume mesh. Go to Remeshing -> Create Volume Mesh (or use the icon in the Remeshing toolbar ). Fill in the dialog with the following parameters: Method: Init and Refine, control edge length ON, Maximum edge length: 5, Shape measure: Height/Base (N) and Shape quality threshold: 0.3. To visualize your volume elements, go to the 3D View Window and in the Active Scene Tab, right-click on Standard Section Y and select Show. 88

91 Mimics Tutorial Check Clip ON and adjust the position of your section. 89

92 Table Of Contents STEP H: You can convert your Tet-4 elements to Tet-10 volume elements. In order to do so, go to Remeshing -> Convert Volume Mesh or select the icon in the Remeshing tab. Select you entity by clicking on your part and select the conversion type Tet4 to Tet10. STEP I: Check the quality of your mesh by going to Remeshing -> Analyze Mesh Quality or by clicking on the icon in the Remeshing tab. Select your volume mesh and check Analyze volume mesh ON. Select the shape measure Height/Base (N) and fill in the quality threshold you want to achieve, in this case 0.3. Select Mark bad triangles, in case you want to visualize the surface triangles in the region of the volume elements with a quality inferior than the value specified in Shape quality threshold and set the element growth to 2. Define a histogram interval of

93 Mimics Tutorial After clicking on Apply, you can find the results of the quality analysis in the log window. When you are satisfied with the quality of the mesh, close the Mimics remesher. You will then return to Mimics and the volume meshes will be automatically loaded in the 3D Objects and FEA mesh tabs in the Project Management. These meshes can then be exported to your FEA software. 4. Material Assignment When you have created a volumetric mesh from your remeshed object, you can perform the material assignment in Mimics. You can see the mesh listed in the FEA mesh tab. 91

94 Table Of Contents Note: We will use grayvalues for this tutorial, so if you are working in Hounsfield units, please change this by going to the Options menu, choose Preferences and change the Pixel Unit in the General tab. With the FEA mesh of the Femur selected, click on the Materials button. Mimics will display a message that the grayvalues for this mesh have to be calculated before you can do a material assignment. Choose Yes to continue. After the calculation you will see following dialog box: 92

95 Mimics Tutorial Mimics shows for each grayvalue the amount of elements that were assigned that particular value. We will then convert this grayvalue to material properties. In this tutorial we will use the uniform method. STEP A: If the uniform method is not selected, click on the radio button next to Uniform. STEP B: Enter the number of materials in the edit box. We will use 10 materials for this tutorial. The FEA module will now divide the range of grayvalues that occur in the volume mesh into 10 equally sized intervals that each represents a material. You can see this discretization by choosing the Materials histogram. Select Limit to Mask: Green 2. The limit assignment to mask intercepts the deviation in the boundary elements due to the partial volume effect. As boundary voxels typically represent multiple tissues by excluding these voxels, the material assignment will become more accurate. 93

96 Table Of Contents STEP C: Enter a density expression to convert the grayvalue of each material to a density. For this tutorial we will use following expression: Density = * Grayvalue. STEP D: Choose to write out only the E-Modulus material properties in the exported file by deselecting the selection boxes before Density and Poisson Coefficient. We will use following expression for the E-Modulus: E-Modulus = * Density. STEP E: Check the values for the materials that will be assigned in the material editor: 94

97 Mimics Tutorial STEP E: Press the OK button to assign the materials to the FEA mesh. The elements of the FEA mesh will be colored according to their materials: 95

98 Table Of Contents This volumetric mesh can then be exported together with the material assignment (in this case only the E-Modulus). 5. Exporting the Volumetric Mesh The volumetric mesh, together with the material assignment can be exported to Ansys, Patran Neutral and Abaqus files and can then be used to do FEA analysis on the mesh. To export the mesh go to the FEA menu and choose Export. Then go to the FEA tab, add the correct mesh to the export list, choose the required format and export directory and click on the OK button. 96

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101 Chapter 9: CFD Tutorial In the CFD Tutorial we will explain the workflow for creating a 3D model of the throat that is suitable to do a CFD analysis on. This tutorial will explain how to link between Mimics and Fluent. We will start with a dataset of a head and explain how to do the segmentation of the airway, how to calculate the 3D model and how to remesh the 3D model. The FEA module has to be licensed to be able to follow this tutorial. The topics that will be discussed in this tutorial are: Importing the images Doing a segmentation Calculating a 3D Object Remeshing the 3D Object Exporting to a Fluent mesh Importing the mesh in Fluent 1. Importing the images In the File menu, select Import Images. Browse to the directory where you have installed the extra Tutorial Files and go to the Airway directory. 99

102 Table Of Contents The images in the Airway directory will be selected automatically, so click on the Next button to accept this selection. In the next step you will see the properties of the project. Make sure that the skip images setting is 0 and that you use CT as compression method. By clicking on the Convert button, the images will be imported and a Mimics project will be created in your default working folder. 2. Doing a segmentation After the import of the images, we can start doing a segmentation of the air in the throat. Create a new mask with a lower threshold value of 1024HU and an upper threshold value of 500HU. 100

103 Index As you can see, this will create a mask that contains all the air in the project. We will now cut of a part of this segmentation to make sure we only have a small part of the throat. To do this, go to the segmentation menu, choose Edit Mask and choose the erase function. Make sure that your cursor is big enough by pressing the CTRL key and drag the left mouse button. Then go to axial slice 48.30/10.80 and remove the green mask from that slice with the manual editing tools. Then do the same for the axial slice 92.70/ Before manual editing After manual editing Before manual editing After manual editing Next we will isolate the throat from the other parts in the dataset. To do this, go to axial slice 63.30/25.80, then go to the segmentation menu and choose the Region Growing tool. Select the Green mask as the source mask and a new mask as the target mask. Then click with the left mouse button on the throat as indicated on the screenshot below. 101

104 Table Of Contents 3. Calculating a 3D Object This will result in a second mask that only contains the throat. You can now calculate a 3D Object. To do this, go to the segmentation menu and select the Calculate 3D Object item. Select the Yellow mask from the list, choose Custom Quality and then click on the Options button. This will open the Calculate 3D Parameters dialog where you should use the same settings as below: 102

105 Index This will result in following 3D: This 3D Object is quite coarse because we are not using any smoothing. We will do this smoothing in the Remesher to make sure that we can contain the sharp edges at the top and bottom of the throat. 4. Remeshing the 3D Object This 3D Object now has to be remeshed in the Mimics Remesher. To do this, go to the FEA menu and choose Remesh. This will show following dialog: Make sure your interface is looking like the screenshot below: 103

106 Table Of Contents 4.1 Mark inlet and outlet Go to the Mark toolbar and select the mark smooth region. Left click on the inlet to mark the area. Then Right click on the marked area and select separate -> Move to new surface. Perform the same procedure on the outlet. Press the Esc key to unselect the mark tool. 104

107 Index To rename the surfaces go to the database tab. Browse to the Surface list of the Yellow 3D. You can rename the surfaces by double clicking on the name. 4.2 Smoothing We will first do a smoothing operation. Since we don t want to lose the sharp edges at the in and out surface, we will only select the wall surface. In the remeshing toolbar select the smoothing tool. To select the wall surface, press left-click on the mantle and select wall from the list. 105

108 Table Of Contents Make sure the Wall is listed as Entity. Click on apply to Smooth the surface. 4.3 Improve quality Next we will improve the quality of the triangles. Make sure that Skewness (N) is selected as Shape measure in the Quality parameter section. In the Histogram section the Current measure should be set to Shape measure: Set a value of 0.4 as the maximum quality measure. As you can see we have 186 triangles with a quality that is below 0.4. Hint: The skewness parameter in the Mimics remesher and the Fluent softwares are inverses. So a quality of 0.4 in the Mimics Remesher is actually a quality of 1-0.4=0.6 in Fluent. We will try to remove these with the Auto Remesh operation. Use following settings and click on OK: 106

109 Index Then apply the Auto-Remesh operation again with following settings: This will result in following 3D Object and quality histogram: 107

110 Table Of Contents As you can see, there are no more triangles with a quality below Sharp Geometry Next we will check for sharp geometries in the part. To do this, select from Inspection measure list the sharp geometry measure. Make sure to put the Current measure to Inspection measure and drag the green slider to 0.8: 108

111 Index Now click on the Mark bad button to select the sharp geometry and click on the Expand Marked Area button. We will refine the mesh where sharp geometry is occurring. You can do this by calling the auto Remeshing algorithm again and by setting a maximum edge length of 0.5mm. Make sure to select marked only. Now, we want to smooth the parts where sharp geometry is occurring, but we don t want to change the sharp edges of the in and outlet surfaces. In the groups section enable the Groups and the Show All checkmarks and set the Boundary level to 1. Select the Shell button on the mark toolbar, hold the Ctrl key and left click on the in and outlet surfaces. 109

112 Table Of Contents Select again the Smoothing function are selected and click on apply., make sure the Marked triangles Click on the Unmark button triangles. in the mark toolbar again to unmark all Go again to the Quality parameter in the quality histogram and you will see that a couple of bad triangles were created during the previous operations. Remove them by using the Split Based Remeshing algorithm again with following settings: 110

113 Index When you are satisfied with the quality of the mesh, close the Mimics remesher. You will then return to Mimics and the remeshed surface mesh can then be exported. 5. Export the mesh to Fluent Now you can export the remeshed 3D object in Mimics to a Fluent mesh. To do this, go to the Export menu and choose Fluent. Select the remeshed 3D and click on add: 111

114 Table Of Contents Click on OK to export the mesh. In the surface split dialog select Use current surface split, this option will preserve the naming of surface split you did in the Mimics remesher. Click on OK to finish the export. 6. Import the mesh in Fluent You can then import this fluent file in fluent by using following parameters: 112

115 Index Chapter 10: Non-manifold Assembly Tutorial The non-manifold assembly Tutorial explains step by step how to obtain matching surfaces between the bone and an implant. First we will register the femoral head prosthesis on the Femur. Secondly we will use the cutting tools of the simulation module to perform an ostectomy of the femoral head. In the Mimics re-mesher we will combine both the femur shaft and the implant to ensure perfectly coinciding nodes between them. The Simulation, FEA and STL+ module have to be licensed to be able to conclude this tutorial. In case you do not have the simulation module you can skip the Ostectomy of the femoral neck and still perform the remeshing part of the tutorial. The topics that will be discussed in this tutorial are: Opening the Project Calculating a 3D Registration of the implant Ostectomy of the femoral neck Remeshing the femur and implant Creating a volume mesh Exporting the remeshed 3D models 1. Opening the project In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Femur.mcs file. 2. Calculating a 3D There is already a yellow mask available in this dataset that will be used to calculate a 3D object. Select the yellow mask and click on the Calculate 3D icon in the Masks toolbar. In the Calculate 3D dialog select the High quality setting and click on calculate. 113

116 Table Of Contents 3. Registration of the implant 3.1 Import the STL In the file menu select import STL (or go to the STL tab in the Project Management and click on Load STL from the tabs toolbar. in the toolbar of the STL tab). From the TutorialData folder load the Implant.stl. 3.2 Point registration The Point registration will be used to bring the implant nearer to the Femur. Indicate a start points on the STL and their corresponding end point on a 3D model or in the 2D views. Mimics will then calculate the transformation matrix that should be applied to have the best fit between the start and end points and applies the transformation matrix on the selected STLs. In the registration menu select the Point Registration. Click on Add point, add a start point on the top of the implant head and put the corresponding end point on the femur head. Place a second set of points on the end of the implant neck and in the middle of the Greater Trochanter top. Position the last set of points on the end of the prosthesis and place the corresponding end point in the middle of the femur shaft in the sagittal view. 114

117 Index 3.3 Reposition the implant The position of the implant can be fine tuned using the reposition tools. In the STL tab select the implant and click on the move tool. In the move dialog select Move along inertia axis from the dropdown box. By grabbing one of the arrows you can move the implant in the direction of the selected arrow. The position of the implant can be verified in both, 2D and 3D views. To visualize the implant in 2D enable the contours by selecting the sunglasses in the contour column of the STL tab. 115

118 Table Of Contents To make the implant visible in the 3D view enable the transparency from the 3D toolbar. The transparency setting of each individual 3D object can be changed by toggling the transparency mode in the 3D and STL tab. Left click on the transparency setting to change to another level of transparency 4. Ostectomy of the femoral head To remove the femoral head we will use the polyplane cut from the Simulation module. From the CMF/simulation menu select cut, polyplane cut. In the simulation dialog select the 3D model of the bone, yellow. To perform the cut click once on the top of the femoral neck, turn the 3D and double click on the bottom. This will create a cutting plane as shown in the images below: 116

119 Index The orientation of the cut can still be modified. Hover over the center of the red arrow, when the cursor changes into the reposition icon, hold the left mouse button. By moving the mouse you can change the orientation of the cutting plane. Hold the left mouse button to change the orientation of the cutting plane To finalize the cut the cutting plane should go completely through the bone. Therefore the depth needs to be increased. In the cut with PolyPlane dialog click on properties. In the properties dialog change the depth to 50 mm. 117

120 Table Of Contents Click on Ok, to finish the cut. The cut will create a new 3D model, PolyplanCut-Yellow. To split this model, go the CMF/simulation menu and select split. In the Split dialog select the PolyplaneCut-yellow 3D model and select largest part. In this way you will only preserve the shaft of the femur. 118

121 Index 5. Remesh of the femur and implant The femur and the implant now have to be remeshed in the Mimics Remesher. To do this, go to the FEA menu and choose Remesh. This will show the following dialog: Select both the implant and the shaft of the femur and click on Ok. The Mimics remesh will open showing three tabs, 3D view, inspection scene of the implant, inspection scene of the femur. We will first combine the femur shaft and the implant. The combined mesh will then be remeshed and split afterwards. 119

122 Table Of Contents 5.1 Create non-manifold assembly To make sure that the common surface between the implant and the bone are identical we will combine both meshes into one mesh. Go to the 3D view and select from the Remeshing menu -> Create nonmanifold assembly (or use the Create non-manifold assembly icon in the remeshing toolbar ). As Main entity select the femur shaft by left clicking on the femur. Now click on Intersecting entity and select the implant. Click on Apply to combine both meshes 120

123 Index 5.2 Create Inspection scene To be able to optimize the combined mesh we will need to create an inspection scene. From the remesh toolbar select the create inspection scene tool. Select the non_manifold_assembly and click on apply. 121

124 Table Of Contents 5.3 Sharp triangle filter First we will remove the sharp triangles using the sharp triangle filter. To reduce the amount of triangles, go to Fixing -> Reduction (or use the reduction icon in the fixing toolbar ). Left click on the 3D model to select it and use following parameters Filter distance: 0.2, Threshold angle 15, Filter mode: Collapse. 122

125 Index 5.4 Smooth Femur Shaft Because the 3D model of the femur will be used for FEA only, you can reduce the amount of detail of its outer surface by smoothing it. In the remeshing tab select the smooth icon. Left click on the shaft to select the surface and use following parameters Smooth factor: 0.7, Number of iterations: 6. Then click Apply. 5.5 Reduce The 3D model contains too many triangles for an FE Analysis. To reduce the amount of triangles, go to Remeshing -> Reduction (or use the reduction icon in the remeshing toolbar ). Left click on the 3D model to select it and use following parameters Method: normal, Flip threshold angle: 15, Geometrical error: 0.1, iterations 5, enable preserve surface contours. 123

126 Table Of Contents 5.6 Auto remesh In the next step we will optimize the triangle shape. In this tutorial we will use the Height/Base shape measurement. Select the Height/Base (N) measure from the shape measurement dropdown box. In the histogram drag the upper slider to 0.3, this is the quality needed in order to generate a volume mesh. 124

127 Index To Auto Remesh the 3D object, make sure that the shape parameter is selected as current measure. Go to Remeshing -> Auto Remesh (or use the Auto remesh icon in the remeshing toolbar ) and use the following parameters: quality threshold: 0.3, geometric error: 0.1, 3 iterations, control triangle edge length OFF. After this operation the mesh will still contain triangles with divergent triangle sizes. To create a uniform mesh you can limit the maximum edge length. Call again the Auto remesh function and apply it with following parameters: quality threshold: 0.3, geometric error: 0.1, 3 iterations, control triangle edge length ON, Maximum edge length 5 mm. 125

128 Table Of Contents 5.7 Quality preserving triangle reduction The mesh still contains groups of small triangles. These can be removed using the quality preserving reduce triangles. Go to Remeshing -> Quality preserve reduce triangles (or use the Quality preserving triangle reduction icon in the Remeshing toolbar ) and use the following parameters: Quality threshold 0.3, number of iterations 3, Max Geometry error 0.3 mm, Max edge length 5 mm. 126

129 Index You now obtained a uniform mesh with the desired quality. 5.8 Creating a volume mesh Now that your surface mesh has an adequate quality, you can create your volumetric mesh. Click on the Create Volume Mesh icon in the Remeshing tab. Select your entity by clicking on your non-manifold assembly. Select Init and Refine as method and check Control edge length ON, specifying a value for Maximum edge length of 5. In Shape measure select Height/Base (N), define a Shape quality threshold of 0.3 and click on Apply. 127

130 Table Of Contents To visualize your volume elements, go to the 3D View window and in the Active Scene Tab, right-click on Standard Section Y and select Show. Check Clip ON and adjust the position of your section. 128

131 Index Close 3-matic to revert to Mimics. 6. Exporting the remeshed 3D models Now you can export the remeshed 3D objects in Mimics to a Patran neutral, Abaqus or Ansys file. To do this go to the Export menu and choose the correct format to export the mesh. Select the FEA meshes and click Add. To export, click OK: 129

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