Mimics Student Edition Course Book HW PDF

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Summary

This is an excersise having to do with biological computer applications yes I said what I said This also talks about how to make 3d models...

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SE Mimics Student Edition Course Book

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Mimics Student Edition Course Book Mimics Student Edition Course Book .......................................................................... 1 / Introduction ............................................................................................................ 3 / Overview ................................................................................................................. 3 Materialise Overview ............................................................................................................. 3 Mimics history ...................................................................................................................... 3 From image to model ............................................................................................................ 3 STL file explanation ............................................................................................................... 3 Segmentation ....................................................................................................................... 4 The applications of Mimics ..................................................................................................... 5 RP ....................................................................................................................................... 5 CAE ..................................................................................................................................... 6 Remeshing ........................................................................................................................... 7 Volume Mesh ....................................................................................................................... 7 Material properties ............................................................................................................... 7 CAD ..................................................................................................................................... 8 Surgical Simulation................................................................................................................ 8 Discussion and Conclusion ...................................................................................................... 9 Before You Start .................................................................................................................... 9 Install Libraries .................................................................................................................................. 9 How to Use this Tutorial .................................................................................................................... 9

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Lesson 1: Mimics Navigation .............................................................................. 10 1.1 1.2

Explanation ..............................................................................................................10 Step by Step Tutorial .................................................................................................12

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

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Homework ...............................................................................................................17

Mimics Lesson 2: Basic Segmentation .............................................................. 18 2.1 2.2

Explanation ............................................................................................................18 Step by Step Tutorial ..............................................................................................18

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

2.3

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Homework..............................................................................................................30

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

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3.1 3.2

Explanation ............................................................................................................31 Step by Step Tutorial ..............................................................................................31

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

3.3

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Homework..............................................................................................................41

Mimics Lesson 4: Surgical Simulation ............................................................... 42 4.1 4.2

Explanation ............................................................................................................42 Step by Step Tutorial ..............................................................................................42

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

4.3

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Homework..............................................................................................................46

Mimics Lesson 5: CAD link.................................................................................. 47 5.1 5.2

Explanation ............................................................................................................47 Step by Step Tutorial..............................................................................................47

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

5.3

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Homework..............................................................................................................55

Mimics Lesson 6: Centerline creation ................................................................ 56 6.1 6.2

Explanation ............................................................................................................56 Step by Step Tutorial ..............................................................................................56

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

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Homework..............................................................................................................61

Mimics Lesson 7: FEA (part 1) ............................................................................ 62 7.1 7.2

Explanation ............................................................................................................62 Step by Step Tutorial ..............................................................................................64

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

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Homework..............................................................................................................71

Mimics Lesson 8: FEA (part 2) ............................................................................ 72 8.1 8.2

Explanation ............................................................................................................72 Step by Step Tutorial ..............................................................................................72

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

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Homework..............................................................................................................80

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Introduction

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

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Overview

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

Mimics history After the start of the company Materialise in 1990 as a rapid prototyping company, it didn’t take long for the company to see the analogy between RP and CT (or MRI) images; in RP, a 3D model is built slice per slice, whereas a CT scanner does the reverse, it breaks down a 3D model (the human body) into a stack of image slices. In 1992 Materialise wrote software that linked the image information to RP models. The software allowed extracting 3D information from an image stack and building a 3D model from it, using RP technology. Materialise’s Interactive Medical Image Control System (MIMICS) was born.

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

STL file explanation An STL file is a triangulated surface mesh file. The file contains the three nodes of each triangle and defines the normal direction of the triangle. This file format is ideal for anatomical geometry because of its

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4 simple file structure and flexibility to match any contour desired. It is not controlled by parametric constraints such as true CAD files and IGES files. Below is an example of the triangulation of an STL file.

Segmentation The medical images coming from CT or MRI scanners consist of grayscale information. Mimics allows the user to create models based on the grayvalues (Hounsfield units in CT images) within these images. A grayvalue is a number associated with an image pixel defining the shade (white, gray, or black) of the pixel. There is a direct association between material density of the scanned object and the grayvalue assigned to each pixel in the image data. Because of this, Mimics has the flexibility to create models from any geometry distinguishable within the scanned data. By grouping together similar grayvalues, the image data can be segmented, and models created. This type of segmentation is called thresholding and yields accurate models. Many of the segmentation tools in Mimics are common in image processing and can be applied in any of the views (XY, XZ or YZ), but Mimics also has a unique 3D editing tool; an initial segmentation can be optimized in a 3D preview (Figure 1). This makes editing very easy, since it allows true editing in 3D, which is easier to comprehend than 2D editing.

Figure 1. Editing a Mimics model in 3D to capture only the femoral head. Using the segmentation and known information on the pixel size and the distance between the...