Mimics 14 Reference Guide

Reference Guide

v14.1.2/ July 2011

Mimics 14.12

1639 July 2011

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/ Table of Contents

PART I ........................................................................................................................ 1 CHAPTER 1: Overview Mimics Modules ............................................................................... 5

Mimics ................................................................................................................................ 5 Import Module .................................................................................................................... 5 RP Slice Module ................................................................................................................. 5 STL+ Module ...................................................................................................................... 5 Pore Analysis Module ......................................................................................................... 6 MedCAD Module ................................................................................................................ 6 Simulation Module .............................................................................................................. 6 FEA/CFD Module ............................................................................................................... 6

CHAPTER 2: Installing Mimics ............................................................................................... 7 CHAPTER 3: Registration ..................................................................................................... 19

1. Register Licenses ......................................................................................................... 19 1.1. Evaluation .............................................................................................................. 19 1.2. License .................................................................................................................. 22

2. Modules ........................................................................................................................ 30 2.1. Password requests ................................................................................................ 30 2.2. System Information ................................................................................................ 30 2.3. Register ................................................................................................................. 31 2.4. Overview of Licenses ............................................................................................. 31

CHAPTER 4: Using Help ....................................................................................................... 33

PART II ..................................................................................................................... 35 CHAPTER 1: User Interface .................................................................................................. 37

1. The Different Views ...................................................................................................... 37 2. Title Bar ........................................................................................................................ 38 3. Menu Bar ...................................................................................................................... 38 4. 3D Toolbar .................................................................................................................... 38

4.1. Toggle transparency .............................................................................................. 39 4.2. Clipping .................................................................................................................. 39 4.3. Volume rendering .................................................................................................. 41 4.4. Show reference planes .......................................................................................... 42 4.5. Select 3D view ....................................................................................................... 43 4.6. Rotate view ............................................................................................................ 43 4.7. 3D locator .............................................................................................................. 44 4.8. Toggle visibility ...................................................................................................... 45 4.9. Show/Hide World Coordinate System ................................................................... 45

5. Indicators in the views .................................................................................................. 45 5.1. Tick Marks ............................................................................................................. 45 5.2. Intersection Lines ................................................................................................... 45 5.3. Slice Position ......................................................................................................... 46 5.4. Orientation strings .................................................................................................. 46

6. The Context Menu ........................................................................................................ 46 CHAPTER 2: Navigation ........................................................................................................ 49

1. 1-Click Navigation ........................................................................................................ 49 2. Pan view ....................................................................................................................... 49 3. Rotate view ................................................................................................................... 49 4. Zoom ............................................................................................................................ 50 5. Zoom to fixed factor ...................................................................................................... 50

6. Zoom to full screen ....................................................................................................... 51 7. Unzoom ........................................................................................................................ 51

CHAPTER 3: Project Management ....................................................................................... 53 1.1. Masks..................................................................................................................... 54 1.2. 3D objects .............................................................................................................. 56 1.3. Polylines ................................................................................................................ 59 1.4. STLs ....................................................................................................................... 60 1.5. Measurements ....................................................................................................... 61 1.6. Reslice Objects ...................................................................................................... 62 1.7. Annotation .............................................................................................................. 63 1.8. Contrast ................................................................................................................. 64 1.9. Volume rendering .................................................................................................. 64 1.10. Clipping ................................................................................................................ 65

CHAPTER 4: Shortcut Keys .................................................................................................. 67 General Shortcuts ............................................................................................................ 67 Shortcuts on files .............................................................................................................. 67 Shortcuts on the views ..................................................................................................... 67 Shortcuts on the 3D view ................................................................................................. 68 Shortcuts on the layouts ................................................................................................... 68 Shortcuts on Segmentation functions .............................................................................. 68

Region Growing ............................................................................................................ 68 Edit ................................................................................................................................ 68 Shortcuts on text fields in dialogs ................................................................................. 68 Shortcuts on Movie Tool ............................................................................................... 69 Shortcuts on Polylines .................................................................................................. 69

CHAPTER 5: CT Gray scale .................................................................................................. 71

PART III .................................................................................................................... 73 CHAPTER 1: File Menu ......................................................................................................... 75

1. New Project Wizard ...................................................................................................... 75 1.1. Selecting images to import .................................................................................... 76 1.2. Importing DICOM images ...................................................................................... 77 1.3. Reading Tiff, Bitmap and Jpeg images .................................................................. 80 1.4. Reading Raw images ............................................................................................. 83 1.5. Excluded images ................................................................................................... 84

2. Open project ................................................................................................................. 85 2.1. List of studies ......................................................................................................... 86 2.2. Functions ............................................................................................................... 87 2.3. List of favorites ....................................................................................................... 87 2.4. Reduce Images ...................................................................................................... 87

3. Save project ................................................................................................................. 88 4. Save project As ............................................................................................................ 88 5. Close project ................................................................................................................ 89 6. Import STL .................................................................................................................... 89 7. STL Library ................................................................................................................... 89 8. Import project ............................................................................................................... 91 9. Organize images .......................................................................................................... 92 10. Change orientation ..................................................................................................... 93 11. Online reslice .............................................................................................................. 94

11.1. Along Curve ......................................................................................................... 94 11.2. Along Plane ......................................................................................................... 96

12. Reslice Project ........................................................................................................... 97 13. Crop Project ............................................................................................................... 98

14. Make project anonymous ......................................................................................... 100 15. Project information ................................................................................................... 100 16. Save/print screenshot ............................................................................................... 101 17. Print .......................................................................................................................... 102

17.1. Properties .......................................................................................................... 103 17.2. Navigation .......................................................................................................... 103 17.3. Print Pages ........................................................................................................ 103 17.4. Functions ........................................................................................................... 103 17.5. Advanced Printing .............................................................................................. 104

18. List of previously opened files .................................................................................. 105 19. Exit ............................................................................................................................ 105

CHAPTER 2: Edit Menu ....................................................................................................... 106 1. Undo ........................................................................................................................... 106 2. Redo ........................................................................................................................... 106 3. Show Undo List .......................................................................................................... 106 4. Copy objects to clipboard ........................................................................................... 106 5. Paste objects from clipboard ...................................................................................... 107

CHAPTER 3: View Menu ..................................................................................................... 109 1. Toolbars ...................................................................................................................... 109

1.1. Main toolbar ......................................................................................................... 110 1.2. Measurements toolbar ......................................................................................... 110 1.3. Segmentation toolbar ........................................................................................... 110 1.4. Navigation toolbar ................................................................................................ 111

2. Status bar ................................................................................................................... 111 3. Project Management .................................................................................................. 111 4. Project Management tabs .......................................................................................... 112 5. Interpolated images .................................................................................................... 112 6. Show/Hide .................................................................................................................. 112 7. Pan view ..................................................................................................................... 113 8. Rotate view ................................................................................................................. 113 9. Zoom .......................................................................................................................... 114 10. Unzoom .................................................................................................................... 114 11. Zoom to full screen ................................................................................................... 114 12. 3D Background color ................................................................................................ 115 13. Toggle gray scale ..................................................................................................... 115 14. Pseudo Colors .......................................................................................................... 115

14.1. Gray ................................................................................................................... 116 14.2. Full Spectrum ..................................................................................................... 116 14.3. Sawtooth ............................................................................................................ 116 14.4. Triangle .............................................................................................................. 117

15. Masks Shade ............................................................................................................ 117 16. Layouts ..................................................................................................................... 118

16.1. Image layout ...................................................................................................... 118 16.2. 3D layout ............................................................................................................ 118 16.3. Reslice layout .................................................................................................... 119

17. Toggle 3D Window ................................................................................................... 119 18. Alignment image ....................................................................................................... 120

CHAPTER 4: Measurements Menu .................................................................................... 123 1. Measure distance ....................................................................................................... 123 2. Measure angle ............................................................................................................ 124 3. Measure diameter ...................................................................................................... 124 4. Shortest distance over surface ................................................................................... 124

5. Measure density in rectangle ..................................................................................... 125 6. Measure density in ellipse .......................................................................................... 126 7. Add Text Annotations ................................................................................................. 126 8. Profile line ................................................................................................................... 127

8.1. Figure ................................................................................................................... 128 8.2. List of profile lines ................................................................................................ 128 8.3. Functions on profile lines ..................................................................................... 128 8.4. Options ................................................................................................................ 128 8.5. Measuring ............................................................................................................ 128

9. 3D Histogram ............................................................................................................. 129 CHAPTER 5: Filter Menu ..................................................................................................... 131

1. Binomial blur ............................................................................................................... 131 2. Curvature flow ............................................................................................................ 132 3. Discrete Gaussian ...................................................................................................... 132 4. Gradient magnitude .................................................................................................... 133 5. Mean ........................................................................................................................... 134 6. Median ........................................................................................................................ 135 7. Show filtered images .................................................................................................. 135 8. Edit filter list ................................................................................................................ 136

CHAPTER 6: Segmentation Menu ...................................................................................... 137 1. Thresholding ............................................................................................................... 137

1.1. With the thresholding toolbar ............................................................................... 137 1.2. With a Profile Line ................................................................................................ 138

2. Region Growing .......................................................................................................... 139 3. Dynamic Region Growing ........................................................................................... 139 4. 3D LiveWire ................................................................................................................ 140

4.1. The 3D LiveWire Interface ................................................................................... 142 5. Morphology Operations .............................................................................................. 142 6. Boolean Operations .................................................................................................... 143 7. Cavity Fill .................................................................................................................... 144 8. Edit Masks .................................................................................................................. 145 9. Multiple slice edit ........................................................................................................ 146

9.1. The multiple slice edit interface ........................................................................... 147 10. Edit Mask in 3D ........................................................................................................ 148 11. Smooth Mask ........................................................................................................... 150 12. Crop Mask ................................................................................................................ 150 13. Calculate Polylines ................................................................................................... 151 14. Update Polylines ...................................................................................................... 152 15. Calculate 3D ............................................................................................................. 152

15.1. Listed masks ...................................................................................................... 153 15.2. Quality ................................................................................................................ 153 15.3. Calculate ............................................................................................................ 153 15.4. Options .............................................................................................................. 153

16. Label ......................................................................................................................... 157 17. Cavity Fill from Polylines .......................................................................................... 158 18. Calculate polylines from 3D ...................................................................................... 158 19. Calculate mask from 3D ........................................................................................... 159

CHAPTER 7: Registration Menu ......................................................................................... 161 1. Point Registration ....................................................................................................... 161

1.1. List of STLs .......................................................................................................... 161 1.2. List of Landmark points ........................................................................................ 161

2. Global registration ...................................................................................................... 162

2.1. List of Movable Part ............................................................................................. 162 2.2. List of Fixed Part .................................................................................................. 163 2.3. Settings ................................................................................................................ 163

3. STL Registration ......................................................................................................... 163 3.1. List of STLs .......................................................................................................... 164 3.2. List of Masks ........................................................................................................ 164 3.3. Settings ................................................................................................................ 164

4. Image Registration ..................................................................................................... 165 4.1. Load in the second dataset ................................................................................. 166 4.2. Landmark Points .................................................................................................. 167 4.3. Fusion Method ..................................................................................................... 167 4.4. Applying the registration ...................................................................................... 168

CHAPTER 8: Export Menu .................................................................................................. 169 1. Dicom ......................................................................................................................... 169 2. 3dd .............................................................................................................................. 169 3. BMP/JPEG ................................................................................................................. 170 4. 2D Mask Area ............................................................................................................. 171 5. Grayvalues ................................................................................................................. 171 6. Txt ............................................................................................................................... 172 7. Capture Movie ............................................................................................................ 173

CHAPTER 9: Options Menu ................................................................................................ 175 1. Register Licenses ....................................................................................................... 175 2. Modules ...................................................................................................................... 175 3. Preferences ................................................................................................................ 175

3.1. General preferences ............................................................................................ 176 3.2. Visualization preferences..................................................................................... 178 3.3. 3D Settings .......................................................................................................... 179 3.4. Masks preferences .............................................................................................. 181 3.5. Predefined Thresholds ......................................................................................... 182 3.6. Import ................................................................................................................... 183 3.7. Nerve ................................................................................................................... 184 3.8. Annotation ............................................................................................................ 185 3.9. Printing preferences ............................................................................................. 186 3.10. Reslicing preferences ........................................................................................ 187 3.11. Advanced SCSI ................................................................................................. 189

CHAPTER 10: Help Menu .................................................................................................... 191 1. General Help .............................................................................................................. 191 2. Context Help ............................................................................................................... 191 3. Tutorial ........................................................................................................................ 191 4. User Community ......................................................................................................... 191 5. About .......................................................................................................................... 191

PART IV .................................................................................................................. 193 CHAPTER 1: Import ............................................................................................................. 195

1. Import licenses ........................................................................................................... 195 2. Reading from Optical Disk .......................................................................................... 195

2.1. Reading from optical disk .................................................................................... 195 2.2. Hardware configuration for SCSI drives .............................................................. 196 2.3. SCSI Troubleshooting .......................................................................................... 198

3. Reading from tape ...................................................................................................... 199 4. Dicom Input Application .............................................................................................. 202

4.1. Installing the DIA .................................................................................................. 202 5. Overview of supported images ................................................................................... 207

5.1. DICOM ................................................................................................................. 207 5.2. BMP, TIFF, JPEG ................................................................................................ 207 5.3. User-defined Import ............................................................................................. 207 5.4. Proprietary Formats ............................................................................................. 207

CHAPTER 2: RP Slice .......................................................................................................... 211 1. Starting RP Slice ........................................................................................................ 211 2. Exporting contour files ................................................................................................ 212

2.1. RP Slice Mask or File selection ........................................................................... 212 2.2. RP Slice/STL+ to CLI, SLI, SLC, IGES ............................................................... 214 2.3. RP Slice Calculation Parameters ........................................................................ 216

3. Support Generation .................................................................................................... 219 4. How to work with sli files on the 3D systems SLA 250? ............................................ 222 5. RP Slice and Lightyear ............................................................................................... 223

5.1. Create a sliced file ............................................................................................... 223 5.2. Generate the support file ..................................................................................... 226 5.3. Open the files in Lightyear ................................................................................... 229

CHAPTER 3: STL+ ............................................................................................................... 231 1. Exporting triangulated files ......................................................................................... 231

1.1. STL+ mask, 3D or file selection ........................................................................... 232 1.2. STL+ - STL / VRML Parameters .......................................................................... 233

2. Modifying triangulated files ......................................................................................... 236 2.1. Smoothing ............................................................................................................ 236 2.2. Triangle Reduction ............................................................................................... 237 2.3. Wrap .................................................................................................................... 238

CHAPTER 4: Pore Analysis ................................................................................................ 238 1. Starting Pore Analysis Module ................................................................................... 239 2. Performing a Pore Analysis ........................................................................................ 239 3. Checking Pore Analysis measurements .................................................................... 241 4. Exporting Pore Analysis measurements .................................................................... 241

CHAPTER 5: MedCAD ......................................................................................................... 243 1. Starting MedCAD ....................................................................................................... 243 2. CAD Objects tab ......................................................................................................... 244

2.1. List of created Objects ......................................................................................... 244 2.2. Functions on Objects ........................................................................................... 244

3. Exporting Iges files ..................................................................................................... 245 3.1. Starting from the Export menu: ............................................................................ 245 3.2. Starting from the Polylines tab page: ................................................................... 245 3.3. Starting from the CAD Objects tab page: ............................................................ 245 3.4. Starting from MedCAD menu: ............................................................................. 246

4. Exporting point cloud files .......................................................................................... 246 4.1. Description of the main areas .............................................................................. 246

5. MedCAD Menu ........................................................................................................... 246 5.1. MedCAD Menu .................................................................................................... 246 5.2. Polyline Growing .................................................................................................. 247 5.3. Point ..................................................................................................................... 248 5.4. Line ...................................................................................................................... 249 5.5. Circle .................................................................................................................... 250 5.6. Sphere ................................................................................................................. 252 5.7. Plane .................................................................................................................... 253 5.8. Cylinder ................................................................................................................ 255 5.9. Splines ................................................................................................................. 256 5.10. Freeform Surfaces ............................................................................................. 259

5.11. Freeform Tree .................................................................................................... 261 5.12. Analyses ............................................................................................................ 266 5.13. Export all object to IGES ................................................................................... 266

CHAPTER 6: FEA/CFD ........................................................................................................ 267 1. Starting the FEA/CFD module .................................................................................... 267 2. FEA Mesh tab ............................................................................................................. 268

2.1. List of created Objects ......................................................................................... 268 2.2. Functions on Objects ........................................................................................... 268

3. FEA Menu................................................................................................................... 269 3.1. FEA menu ............................................................................................................ 269 3.2. Calculate Non-Manifold ....................................................................................... 269 3.3. Remesh ............................................................................................................... 270 3.4. Create mesh ........................................................................................................ 270 3.5. Material ................................................................................................................ 272 3.6. Import ................................................................................................................... 272 3.7. Export................................................................................................................... 273

4. Calculate Non-Manifold .............................................................................................. 274 5. Remeshing ................................................................................................................. 277

5.1. Remeshing Protocol ............................................................................................ 277 6. Material Assignment ................................................................................................... 280

6.1. Material assignment method ............................................................................... 282 6.2. Material Expressions ........................................................................................... 286 6.3. Material Editor ...................................................................................................... 287

7. Using Mimics with Patran ........................................................................................... 288 7.1. Export a volumetric file to Patran ......................................................................... 288 7.2. Export a surface file to Patran ............................................................................. 289 7.3. Import a mesh in Patran ...................................................................................... 290 7.4. Export the volume mesh from Patran .................................................................. 291 7.5. Import the Patran volume mesh in Mimics .......................................................... 292

8. Using Mimics with ABAQUS ....................................................................................... 293 8.1. Export an ABAQUS volume mesh ....................................................................... 293 8.2. Import a mesh in ABAQUS .................................................................................. 294 8.3. Export the volume mesh from ABAQUS .............................................................. 295 8.4. Import the ABAQUS volume mesh in Mimics ...................................................... 297 8.5. The ABAQUS file ................................................................................................. 297

9. Using Mimics with Ansys ............................................................................................ 299 9.1. Export a volumetric file to Ansys ......................................................................... 299 9.2. Import a mesh in Ansys ....................................................................................... 300 9.3. Export the volume mesh from Ansys ................................................................... 304 9.4. Import an e volume mesh in Mimics .................................................................... 304 9.5. The PREP7 file .................................................................................................... 306 9.6. The nodes file ...................................................................................................... 307 9.7. The elements file ................................................................................................. 307 9.8. Supported element types ..................................................................................... 308 9.9. Supported material properties ............................................................................. 308 9.10. Supported PREP7 commands ........................................................................... 308

10. Using Mimics with Ansys Workbench ...................................................................... 309 10.1. Export to Ansys workbench ............................................................................... 309 10.2. Import in Ansys workbench ............................................................................... 309

11. Using Mimics with Simmetrix.................................................................................... 315 11.1. Export a volumetric file from Mimics .................................................................. 315 11.2. Change the Abaqus pattern in Simmetrix .......................................................... 316

11.3. Import Simmetrix files in Mimics ........................................................................ 317 12. Using Mimics and Fluent .......................................................................................... 318

12.1. Export the object to a Fluent file ........................................................................ 318 12.2. Import the surface mesh in Fluent ..................................................................... 319 12.3. Convert the surface mesh to a volume mesh .................................................... 320

13. Empirical Expressions .............................................................................................. 320 13.1. Expressions for Trabecular/Cancellous Bone ................................................... 320 13.2. Expressions for Cortical Bone ........................................................................... 322 13.3. Legend ............................................................................................................... 323 13.4. References ........................................................................................................ 324

CHAPTER 7: Simulation ...................................................................................................... 325 1. Starting Simulation ..................................................................................................... 325 2. Simulation tab ............................................................................................................. 325 3. Simulation Menu ......................................................................................................... 327

3.1. Measure and Analyse .......................................................................................... 327 3.2. Cut ....................................................................................................................... 337 3.3. Split ...................................................................................................................... 342 3.4. Reposition ............................................................................................................ 343 3.5. Place Distractor ................................................................................................... 346 3.6. Reposition with Distractor .................................................................................... 348 3.7. Soft tissue ............................................................................................................ 349 3.8. Advanced tools .................................................................................................... 352

4. Tools Menu ................................................................................................................. 358 4.1. Smoothing ............................................................................................................ 358 4.2. Triangle Reduction ............................................................................................... 359

5. Nerves toolbox ........................................................................................................... 360 5.1. Draw a nerve ....................................................................................................... 360 5.2. Select a nerve ...................................................................................................... 360 5.3. Delete a nerve ..................................................................................................... 360 5.4. Add a point to a nerve .......................................................................................... 361 5.5. Remove a point from a nerve .............................................................................. 361 5.6. Show the list of nerves ......................................................................................... 361

PART V ................................................................................................................... 363 CHAPTER 1: Import ............................................................................................................. 367

1. Automatic import ........................................................................................................ 367 2. Organizing images ..................................................................................................... 369 3. Semi-automatic import ............................................................................................... 370

CHAPTER 2: Mimi ................................................................................................................ 373 1. Opening the project .................................................................................................... 373 2. Windowing .................................................................................................................. 374 3. Thresholding ............................................................................................................... 375 4. Region growing .......................................................................................................... 376 5. Creating a 3D representation ..................................................................................... 376 6. Displaying a 3D representation .................................................................................. 377 7. STL+ procedures ........................................................................................................ 378

7.1. Generating a STL file ........................................................................................... 378 8. RP Slice procedures ................................................................................................... 379

8.1. RP Slice procedures ............................................................................................ 379 8.2. Generating a contour file ..................................................................................... 379 8.3. Generating supports ............................................................................................ 381

9. View of end result ....................................................................................................... 384 CHAPTER 3: Simon ............................................................................................................. 385

1. Opening the project .................................................................................................... 385 2. Preparation of the data ............................................................................................... 385

2.1. Windowing ........................................................................................................... 385 2.2. Thresholding ........................................................................................................ 385 2.3. Region growing .................................................................................................... 386 2.4. Editing - Thresholding .......................................................................................... 386 2.5. Boolean Operations ............................................................................................. 394

3. View of end result ....................................................................................................... 394 CHAPTER 4: Hip .................................................................................................................. 395

1. Opening the project .................................................................................................... 395 2. Preparation of the data ............................................................................................... 395

2.1. Thresholding ........................................................................................................ 395 2.2. Region growing .................................................................................................... 395

3. Calculation of the Polylines ........................................................................................ 396 4. Patching of contours ................................................................................................... 396 5. Creation of MedCAD objects ...................................................................................... 398 6. Visualization possibilities ............................................................................................ 400

CHAPTER 5: Obturator ....................................................................................................... 401 1. Case study.................................................................................................................. 401

1.1. Obturator prosthesis for oncologic patients ......................................................... 401 2. Preparation of the data ............................................................................................... 403

2.1. Preparation of the data ........................................................................................ 403 2.2. Windowing ........................................................................................................... 403 2.3. Orientation ........................................................................................................... 403 2.4. Thresholding ........................................................................................................ 403

3. Editing ......................................................................................................................... 405 4. Region growing .......................................................................................................... 407 5. View of end result ....................................................................................................... 409

CHAPTER 6: Import Raw images ....................................................................................... 411 1. Raw import ................................................................................................................. 411

1.1. Import images ...................................................................................................... 411 2. Edit images ................................................................................................................. 413

CHAPTER 7: Simulation ...................................................................................................... 415 1. Opening the project .................................................................................................... 415 2. Windowing .................................................................................................................. 415 3. Thresholding ............................................................................................................... 415 4. Region Growing .......................................................................................................... 416 5. Calculating a 3D ......................................................................................................... 417 6. Cutting ........................................................................................................................ 418 7. Splitting ....................................................................................................................... 421 8. Mirroring ..................................................................................................................... 422 9. Repositioning .............................................................................................................. 424

CHAPTER 8: FEA ................................................................................................................. 427 1. Opening the project .................................................................................................... 427 2. Calculating a 3D ......................................................................................................... 427 3. Remeshing the 3D ...................................................................................................... 427

3.1. Remeshing Protocol ............................................................................................ 429 4. Material Assignment ................................................................................................... 435 5. Exporting the Volumetric Mesh .................................................................................. 439

CHAPTER 9: CFD ................................................................................................................. 441 1. Importing the images .................................................................................................. 441 2. Doing a segmentation ................................................................................................ 441

3. Calculating a 3D Object .............................................................................................. 442 4. Remeshing the 3D Object .......................................................................................... 443

4.1. Mark inlet and outlet ............................................................................................ 444 4.2. Smoothing ............................................................................................................ 445 4.3. Improve quality .................................................................................................... 446 4.4. Sharp Geometry .................................................................................................. 448

5. Export the mesh to Fluent .......................................................................................... 451 6. Import the mesh in Fluent ........................................................................................... 452

CHAPTER 10: Non-Manifold Assembly ............................................................................. 453 1. Opening the project .................................................................................................... 453 2. Calculating a 3D ......................................................................................................... 453 3. Registration of the implant .......................................................................................... 453

3.1. Import the STL ..................................................................................................... 453 3.2. Point registration .................................................................................................. 453 3.3. Reposition the implant ......................................................................................... 454

4. Ostectomy of the femoral head .................................................................................. 455 5. Remesh of the femur and implant .............................................................................. 457

5.1. Create non-manifold assembly ............................................................................ 458 5.2. Create Inspection scene ...................................................................................... 459 5.3. Sharp triangle filter ............................................................................................... 460 5.4. Smooth Femur Shaft ............................................................................................ 461 5.5. Reduce ................................................................................................................ 461 5.6. Auto remesh ........................................................................................................ 462 5.7. Quality preserving triangle reduction ................................................................... 463 5.8. Creating a volume mesh ...................................................................................... 464

6. Exporting the remeshed 3D models ........................................................................... 465

PART VI .................................................................................................................. 467 CHAPTER 1: System Requirements .................................................................................. 469

Minimal Requirements: ................................................................................................... 469 Software: ..................................................................................................................... 469 Hardware: ................................................................................................................... 469

Recommended: .............................................................................................................. 469 Software: ..................................................................................................................... 469 Hardware: ................................................................................................................... 469

CHAPTER 2: Frequently Asked Questions ....................................................................... 471 Import module ................................................................................................................ 471 STL+ ............................................................................................................................... 472 General ........................................................................................................................... 473

CHAPTER 3: ITK Disclaimer ............................................................................................... 475 CHAPTER 4: Contact Info ................................................................................................... 477

PART I

Introduction

Mimics 14.1 Reference Guide

3

Mimics interfaces between scanner data (CT, MRI, Technical scanner,...) and Rapid

Prototyping, STL file format, CAD and Finite Element analysis. The Mimics software is an

image-processing package with 3D visualization functions that interfaces with all common

scanner formats.

Additional modules provide the interface towards Rapid Prototyping using STL or direct layer

formats with support. Alternatively, an interface to CAD (design of custom made prosthesis

and new product lines based on image data) or to Finite Element meshes is available.

Materialise' Interactive Medical Image Control System (MIMICS) is an interactive tool for

the visualization and segmentation of CT images as well as MRI images and 3D rendering of

objects. Therefore, in the medical field Mimics can be used for diagnostic, operation planning

or rehearsal purposes. A very flexible interface to rapid prototyping systems is included for

building distinctive segmentation objects.

The software enables the user to control and correct the segmentation of CT-scans and MRI-

scans. For instance, image artifacts coming from metal implants can easily be removed. The

object(s) to be visualized and/or produced can be defined exactly by medical staff. No

technical knowledge is needed for creating on screen 3D visualizations of medical objects (a

cranium, pelvis, etc.)

Separate software is available to define and calculate the necessary data to build the medical

object(s) created within Mimics on all rapid prototyping systems.

The interface created to process the images provides several segmentation and visualization

tools.


5

CHAPTER 1: Overview Mimics Modules

Mimics consists of seven modules. The image below shows the links between the main

program and its modules.

Mimics Mimics interactively reads CT/MRI data in the DICOM format. Segmentation and editing tools

enable the user to manipulate the data to select bone, soft tissue, skin, etc. Once an area of

interest is separated, it can be visualized in 3D. After this visualization, a file can be made to

interface with STL+ or MedCAD. CAD data, imported as STL files, can be visualized in 2D

and 3D for design validation based on the anatomical geometry.

Import Module Import module imports CT and MRI data from a wide variety of scanner formats. The data can

be accessed from CD, optical disk, DAT tapes, 4 mm tapes, etc.

RP Slice Module RP Slice module provides an interface to Rapid Prototyping systems via sliced files with

patented support structure generation. The perforated support structures are generated in no

time and use less material.

Supported formats:

Common Layer Interface Files (*.cli)

3D Systems Layer Interface Files (*.sli)

3D Systems Contour Files (*.slc)

STL+ Module STL+ module provides interface options via triangulated formats.

6

Supported formats:

STL (ASCII and Binary)

DXF

VRML

PLY

Pore Analysis Module Pore Analysis Module provides a complete characterization of a porous material, including

measurements such as porosity, average pore size, pore interconnectivity, chamber pore size

distribution, throat pore size and specific surface area.

MedCAD Module MedCAD module provides a direct interface to CAD systems via surfaces, curves, and

objects exported as IGES files.

Supported files:

B-Spline (NURB) curves and surfaces exported as IGES

Point Cloud

Simulation Module The Simulation module is an open platform for surgical simulations. You can perform a

detailed analysis of your data using the anthropometric analysis, plan osteotomies and

distraction surgeries or simulate and explain a surgical procedure for your implant design.

FEA/CFD Module The FEA/CFD module provides a link to FEA (Finite Element Analysis) and CFD

(Computational Fluid Dynamics) simulation.

Supported formats:

Patran Neutral

Abaqus

Ansys

Fluent

Nastran


7

CHAPTER 2: Installing Mimics We recommend that you close all other applications before installing Mimics. You must have

administrative privileges to install the software. Place the Mimics CD into your CD-ROM drive.

Make sure the artwork faces up. The autorun starts automatically. If the autorun does not start

automatically, browse to your CD-drive and choose autoplay or double-click on

„MimicsSetup.exe‟.

During the installation the following dialogs will be shown:

STEP 1:

Wait until the Windows installer is ready to start the installation. You will automatically go to

step 2.

STEP 2:

Click Next to proceed.

8

STEP 3:

After reading the license agreement, select the “I accept the terms of the License Agreement”

checkbox and click on the Next button.


9

STEP 4:

Select your region and click Next.

10

STEP 5:

Choose for the Complete or Custom setup type and select where Mimics will be installed.

Mimics will be installed in C:\Program Files\Materialise\Mimics 14.0 by default. If you prefer

another directory, click on the Browse button and select an existing directory out of the list.

Click Next to proceed.

If you have chosen the Complete setup, you will immediately go to Step 7. If you have

chosen the Custom option, you will go to Step 6.


11

STEP 6:

Select if you want to install the Demo Files or not and click on Next.

12

STEP 7:

If you have chosen to install the Demo Files, you can choose where these demo files should

be installed. Mimics will store the studies in a folder C:\MedData by default. If you want to

change this directory, select Browse and go to the folder where you want to store your data.


13

STEP 8:

You can check all the selections made in the previous steps. If everything is filled in like you

want, click Next to proceed. If you want to change or review something, click Back.

14

STEP 9:

You can now start the installation. If you want to change or review something, click Back. If

you want to begin the installation, click Install.


15

STEP 10:

The Mimics software gets installed. This can take a few moments. This window will close

automatically when the progress bar is finished.

16

STEP 11:

After the software has successfully installed, you will see the following message. Click OK.

STEP 12:

Next you will see a message indicating that changes will be made after the next reboot. Click

OK. It‟s recommended to reboot your computer to finalize the installation.


17

To uninstall Mimics, go to Start > Settings > Control panel > Add/Remove programs.

Select Mimics 14.0 and click the Remove button. All Mimics folders and the desktop icon will

be removed.

Note: The installation of the DICOM Input Application and of the Distractor and Anthropometric template libraries are separate processes. The libraries have to be installed separately in order for the Simulation module to function correctly.


19

CHAPTER 3: Registration

To start Mimics, double click the Mimics icon on your desktop or go via the Start button

to Programs, Materialise and choose to start Mimics.

1. Register Licenses Materialise Software is key protected. When you start Mimics for the first time or when your

key has expired, the Key Request Wizard will automatically start up to assist you in

registering. You will be presented with the following options to apply for key files:

1.1. Evaluation

Pick this choice if you want to evaluate the software or if you want to enter an evaluation key

file.

1.1.1. Request a key file

To request a key file select the first option and press Next

20

You will be requested to fill in your contact details. Fill them in as required and click on Next

to continue.

In the next detail dialog fill in the additional required contact details:


21

Once you finish filling in your contact details, a confirmation message will be displayed.

By clicking Finish, your e-mail client will open with a filled-in e-mail message. Just click on

“Send” to forward the message to a Materialise office.

1.1.2. Entering a key file

When you select to enter a key file you will end up in the following dialog:

22

Browse to the location where the key file is stored. When you‟ve entered your key file, the

Next button will become enabled. When you press it, the key file you entered will be verified

and if it is valid, your software will be licensed and the success dialogue will be shown:

1.2. License

If you are a Mimics licensed user, select the second option to apply for a key file or to activate

your Mimics software.


23

1.2.1. Request a License key file

To request a key select the first option.

Three different methods are available to request your license key file.

a. Online activation

If you are interested in having Mimics obtain its license online, select the first option.

24

In the next window you will need to indicate your CCKey.

You can allow Mimics to update the licenses automatically when the check box in the above

window is selected. When the license is about to end, Mimics will automatically contact

software administrator and a new license is generated. You can find your CCkey on the

Certificate of Authenticity.


25

Note: The automatic license renewal only works for local licenses. Floating licenses should be updated in the Floating license Administrator

b. Email request

When you select to request a password by e-mail, you will be asked to fill in your contact

details. Fill them in as required and click on Next to continue.

In the next detail dialog fill in the additional required contact details:

26

When you press the Next button, your e-mail client will open with a filled-in e-mail message.

Just click on “Send” to forward the message to a Materialise office.

c. Website key generation

If you want to generate a key file on Materialise website, select the third option and click Next.

By pressing Finish you will open the Materialise website for password generation. You will

need to indicate your CCKey to login. You can find your CCkey on the Certificate of

Authenticity.


27

Note: The automatic license renewal only works for local licenses. Floating licenses should be updated in the Floating license Administrator

1.2.2. Enter a key file

To register a key file received by Fax or e-mail, select the second option. Browse to the

location of the key file and click on Next.

The key file you entered will be verified and if it is valid, your software will be licensed and the

success dialogue will be shown:

28

1.2.3. Use a floating license server

Pick this option to connect to a floating license server if you have one available. The Floating

License Server Manager dialog will be shown.

To add a new floating license server, click on the Add a server button. This will open the

following dialog:


29

In this dialog you can fill in the IP Address or hostname, IP Port and Description for the

floating license server. You can also browse for a server by clicking on the Browse button.

With the browse function you can browse your Network Places, select the appropriate floating

license server and by clicking on the OK button, the name of this server will be filled in

automatically.

To remove a floating license server from the list, select the server and click on the Remove

selected server button.

To change a floating license server, select the server in the list and click on the Edit the

selected server button.

30

2. Modules You can find an overview of the license information in the Options | Modules dialog.

The dialog exists out of four sections:

2.1. Password requests

This option enables the automatic password update system. To disable it uncheck the

checkbox.

2.2. System Information

In the System Information section of the License information dialog you can find your

SystemID and your CCKey (if filled in).

2.2.1. System ID


31

Your SystemID is a unique identifier for your pc. This ID is dependent on your hardware and

will be used to generate a password.

2.2.2. CCKey

The CCKey is a unique identifier for your software license. You can use this key for

generating passwords with our on-line password generation system. The CCKey can be

found on your Certificate of Authenticity that you will receive when you buy the software (so

evaluators don't have a CCKey). It is optional to fill in the CCKey, but we advise you to do this

because this will facilitate the password generation process.

2.3. Register

Here you can enter a password you received by e-mail. To register, copy the password in the

password field and click on Register.

2.4. Overview of Licenses

This section gives you an overview on the modules that are available for your software. The

name, version, type of license, days left and a comment is displayed for each module.

If you haven't got a password for a certain module, there will appear n/a as number of days

left and "no license found for this module" will be displayed under the comments section.


33

CHAPTER 4: Using Help Mimics provides help so that you can get useful information while you are working. The help

pages contain a description of each command and dialog box, and explains procedures for

most tasks. To get help, press F1 or select Help | General Help from the menu bar. The Help

window consists of a tabbed window showing a tree of topics at the left side and a preview

window at the right side. If the page is not displayed completely, maximize the help window or

scroll with the scroll bars.

You can search for the correct help page in 4 different ways:

Browse through the tree by clicking on the book icons and page icons.

Click on an underlined item in the preview page to jump to the help page about that item.

The tree will be updated accordingly.

Select the Index tab and type the first few letters of the topic you're looking for. The

corresponding items will be highlighted in the list while typing. Click the Display button to

view the item that is highlighted.

To search very quickly all pages about a specific topic, click on the Search tab and fill in

the name of the topic. Click the List topics button to show a list of all help pages about

the topic. Click on an item in the list to view the page.

To hide the contents window. Once it's hidden you can show it again by clicking again on

this button.

To display the previous page.

To display the next page.

To print the current page.

35

PART II

General Information


37

CHAPTER 1: User Interface

1. The Different Views In the default configuration the images appear in a four-dimensional engineering view. The

images in the top right view are called the axial images (XY-view or Top-view) and are

surrounded by a red border. The upper left view (surrounded by an orange border) shows the

coronal images that are the images resliced in the XZ-direction (Front-view). The lower left

view (surrounded by a green border) shows the sagittal images that are the images resliced in

the YZ-direction (Side-view). The lower right view (surrounded by a light-green border) shows

the 3D view.

These windows can be resized by moving the edge between the images (Click and drag to

move this edge).

Image Color

Axial Red

Sagittal Green

Coronal Orange

3D view Light-green

Parallel Yellow (these images are only visible after performing an online reslice)

Cross-sectional Blue (these images are only visible after performing an online reslice)

The other images that can be shown are:

Alignment image (if available)

X-ray image

38

2. Title Bar The title bar displays some information about the project:

The name of the patient and the name of the project are displayed first (unless you have

chosen to anonymize the project and hide the file name) and after the patient name, the

compression of the project is displayed. There are several different types of compression

possible:

Displayed in title bar: Case:

Lossless Compression No compression was used while importing and

JPEG compression was not used during saving

CT Compressed CT compression was used while importing and


MR Compressed MR compression was used while importing and


Air Compressed Cut Air compression was used while importing and


Lossy JPEG Compressed No compression was used while importing and

project was saved with JPEG compression

Lossy JPEG & CT Compressed CT compression was used while importing and


Lossy JPEG & MR Compressed MR compression was used while importing and


Lossy JPEG & Air Compressed Cut Air compression was used while importing and


3. Menu Bar Almost all functions can be accessed via the menus of the menu bar. Corresponding to some

of these functions, you will find buttons on the toolbars.

4. 3D Toolbar The 3D toolbar is displayed at the right side of the 3D view.


39

4.1. Toggle transparency

You can show the 3D object opaque or transparent. Click on the button in the 3D toolbar

to toggle between opaque and transparent view.

Transparency off Transparency on

You can change the transparency of the 3D object and make objects transparent. Drag the

Transparency slider at the bottom of the 3D properties dialog. If the slider is all the way to the

right, the 3D surface is opaque and nothing below the surface can be visualized. If the slider

is all the way to the left, the 3D surface is completely transparent.

4.2. Clipping

Clipping allows you to visualize the section in which you are interested. It can be used, to

evaluate the gray values on the section boundaries or to look inside the model to get a better

comprehension of the geometry. The section can be made along the different planes, axial,

coronal and sagittal. Several clipping planes can be activated at the same time enabling you

to isolate the part of interest.

To enable clipping click on the Enable/Disable Clipping button . The settings of the

clipping can be changed in the clipping tab:

Active

By default one axial clipping plane is active. To make more planes active, make sure to check

the active icon .

40

Clipping in the Axial

Plane

Clipping in the Sagittal

Plane

Combined Axial and

Sagittal Clipping Planes

The position of the clipped plane in the 3D view corresponds with the position of the active

axial, sagittal or coronal image. Scrolling through the 2D images updates the clipped plane in

3D. Also navigation on the clipped 3D is possible by clicking on visible parts on the 3D. When

you rotate the 3D along the clipped plane, the visibility automatically reverses.

Type

As stated above you can select multiple clipping planes. For each view you can define two

clipping planes. For each of the clipping planes, you can choose which objects need to be

clipped. You can choose this by selecting the clipping plane in the list and changing the

selections in the dropdown menu . All objects are selected by default.

Clipping along two axial and a sagittal

plane

Clipping along the axial and sagittal

plane

Clip

By default the direction of the clipping plane is defined by the viewing angle. The direction of

the clipping plane can be locked by selecting a clip direction. Click on the clip icon to lock

to a clipping direction or to unlock.

Lock

The location of the clipping plane is locked to the slice position. To unlock the clipping plane

from the slice position, disable the lock icon . When the lock icon is disabled, you can

determine the location of the clipping plane with the slider at the bottom of the clipping tab.

Texturing

You can also choose between three texturing methods:


41

No texturing Object texturing Full slice texturing

When choosing No texturing, only the 3D Object is clipped and you can see inside the 3D

Object. When choosing Object texturing, a texture corresponding with the 2D slice is placed in

the contours of the 3D Objects. When choosing Slice texturing, the 3D Object is not clipped,

but the whole 2D slice is visible in the 3D window.

Note: This technique is only available in OpenGL and direct3D rendering (not in software). To check your rendering option, go to Option | Preferences and select the OpenGL or Direct3D rendering option in the 3D settings. To accelerate the performance of clipping, activate the hardware acceleration in the same dialog.

4.3. Volume rendering

Volume rendering allows you to quickly visualize your 2D image data as a 3D object without

any segmentation. The 3D object is build up out of the voxels representing the dataset. The

transparency of the voxels is determined based on their grey value. Volume rendering is a

pure visualisation tool and cannot be used for anything else (e.g. exporting).

You can find the interface for the volume rendering in the volume rendering project

management tab:

Defining the opacity

This interface shows a histogram which represents the gray values or Hounsfield units of the

dataset. The transparency of the gray values is set by the opacity lines on the histogram. The

higher a line is positioned the more opaque the voxels within that range will be visualised.

In the first column the line representing the low Hounsfield values is positioned to the bottom.

Subsequently the voxels are represented transparent. In the second column the line is

positioned higher which makes the voxels opaque.

42

Move a point

Position a point click left and drag the point to its new position

Add a point

Click left on a line to add an extra point

Delete a point Right click on a point and select delete to delete a point

Defining the color

The graph below the histogram defines the color of the rendered voxels. You can choose a

color for each point in the graph by right-clicking on the points and choosing Change Color.

Mimics will then create an interpolated shading between the different control points. The

same system for adding, moving and deleting bullets is available as for the opacity line.

Predefined settings

On the bottom of the volume rendering interface you find a dropdown list with predefined

settings. The predefined settings are optimized for CT image and allow you to quickly select

bone, soft tissue or both

You can save your current setting as a predefined setting by clicking on the save button. To

delete your predefined setting, select it from the dropdown box and click on the delete button.

4.4. Show reference planes

It is possible to show in the 3D view the reference planes of the current position by clicking on

the Show Reference Plane button . The reference planes take over the colors that

belong to the different views:

Axial Red

Coronal Orange

Sagittal Green


43

Cross Sectional Blue

Parallel Yellow

The reference planes that have to be shown can be selected in the 3D tab of the Preference

settings. Only the reference planes of the views that are displayed can be shown in the 3D

view.

4.5. Select 3D view

When you click on Select 3D View button , a list with all possible default views is

displayed. Selecting an item from this list will position the 3D object according to the selected

position.

4.6. Rotate view

The rotate function is only available on a 3D object. There are different ways to select the

rotate function:

right-drag with your mouse button

44

use the arrows-keys for precise rotation

use Home / End to rotate 10 degrees Left / Right

use Page Up / Page Down to rotate 10 degrees Up / Down

right-click in the 3D view and select Rotate View from the context menu

click on the Rotate View button in the toolbar

select View > Rotate View from the menu bar

4.7. 3D locator

The 3D locator indicates on the 3D where you are in the 2D. You can activate the 3D locator

by clicking on the 3D locator button .

In the visualization preferences you can choose the 3D locator to be a Dataset position

locator or an Intersection position locator. The Dataset position locator will indicate the

intersection of the views and the full range of the dataset, whereas the Intersection position

locator will only indicate the intersection

Dataset Position Locator Intersection position locator


45

4.8. Toggle visibility

By toggling the 3D representations in the 3D toolbar, you can make the 3D objects visible or

invisible. For every 3D object in the project there is a corresponding miniature.

4.9. Show/Hide World Coordinate System

This button allows you to hide or show the indicator of the World Coordinate System in your

project. The origin of the World Coordinate System depends on the patient coordinates

imported from the DICOM files. During image import, the X and Y coordinates are set to zero

while the Z coordinates are kept as in the DICOM header.

5. Indicators in the views On the different views you can see intersection lines, tick marks, slice positions and

orientation strings. To hide the intersection lines, tick marks or slice positions, select its entry

in View menu > Indicators. Select again its entry to show it again. If you never want to see

one or more indicators when loading a project, select Preferences from the Options menu and

go to the Visualization tab. In this dialog you can make your selection of these indicators.

5.1. Tick Marks

The set of red tick marks to the left of the sagittal and coronal images reference the position

of each axial image in the study. The set of green tick marks below the axial images reference

the position of each sagittal image in the study. The set of orange tick marks to the left of the

axial images reference the position of each coronal image in the study.

Tick marks on Tick marks off

In the View menu, the preference setting for tick marks can be temporarily overruled. If you

prefer another setting permanently, go to Options > Preferences > Visualization.

5.2. Intersection Lines

In the View menu, the preference setting for intersection lines can be temporarily overruled. If

you prefer another setting permanently, go to Options > Preferences > Visualization. The

relation between the different views is indicated by the colors of the intersection lines (dashed

or full colored lines over the view). When you move to a new position, the intersection lines

will be updated and show you your current position in the data set. They are in the matching

color of the corresponding view. Notice the red horizontal line across the sagittal and coronal

images. It references the exact location of the axial image.

When you move to a new position, the intersection lines will be updated and show you your

current position in the data set.

46

After performing an online reslice, you will see 3 blue dashed or full lines and a yellow dashed

or full line in the axial image. The middle blue line references the exact location of the cross-

sectional image (surrounded by a blue border). The most left blue line reference the exact

location of the cross-sectional image at the left top corner of the cross-sectional grid. The

most right blue line reference the exact location of the cross-sectional image at the right

bottom corner of the cross-sectional grid. The yellow line reference the exact location of the

parallel image that is displayed.

Color Table

Axial Red

Cross-section Blue (only visible if the project is resliced in Reslice Layout)

Parallel Yellow (only visible if the project is resliced in Reslice Layout)

Sagittal Green

Coronal Orange

Note: You can choose between dashed or full lines in the Visualization tab of the Preferences window.

5.3. Slice Position

In the view that contains the scanner images, the slice position is indicated in the lower left

corner and the image number is indicated in the lower right corner. In the other views, the

slice position is indicated in the lower right corner.

Image Numbering

Axial Increasing from bottom to top

Sagittal Increasing from the right to the left side of the patient

Coronal Increasing from posterior to anterior

5.4. Orientation strings

The colored letters located on each view shows the orientation of the images.

P : Posterior

A : Anterior

L : Left

R : Right

T : Top

B : Bottom

Looking at the images you can verify if they are correct, if not you can easily change them in

the Change Orientation window going to File > Change Orientation.

6. The Context Menu If you right-click with your mouse on any of the views, you will see the context menu. The

functions in the context menu can differ, depending on the location you click on: if you right-

click on an image, on the 3D view, on a 3D object, a STL, a CAD object, ...


47

There are several easy shortcuts available from the default context menu:

Pan View Enables the panning mode

Zoom Enables the zoom mode

Unzoom Unzooms the view

Zoom to full screen Zooms the view to full screen

3D Window Enables the 3D view in the window


49

CHAPTER 2: Navigation

1. 1-Click Navigation 1-click navigation is very easy. By clicking once on an image (e.g. the axial image) with your

left mouse button all images are immediately updated to show the same point. Navigation is

also possible from the 3D image.

During operations you can still access the 1-click navigation function by pressing the SHIFT

button. This allows you to use the 1-click navigation while editing a mask, cropping a mask….

2. Pan view Every image and 3D view can be panned or moved. When you select the pan function, the

cursor will change to a cross-shaped double arrow. There are different ways to select the pan

function:

hold down the SHIFT key, right-drag your mouse button

right-click in an image or in the 3D view and select Pan View from the context menu

click on the Pan View button in the toolbar

hold down the SHIFT key in combination with the arrows-keys for precise rotation

Hold down the SHIFT key in combination with Home / End for quick Left / Right panning

select View > Pan View from the menu bar

3. Rotate view The rotate function is only available on a 3D object. There are different ways to select the

rotate function:








50

There are two different modes when rotating the 3D view. When your mouse cursor is in the

middle of the 3D window and you then hold down the right mouse button, the 3D view turns

about a vertical axis when you move the mouse left and right. The 3D view tilts around a

horizontal axis if you move the mouse up and down.

When your mouse cursor is at the side of the 3D window and you then hold down the right

mouse button, the 3D view rotates around an axis perpendicular to your screen when moving

the mouse.

4. Zoom Allows to Zoom in at a user defined rectangle. Click on the left mouse button to indicate a

corner of the zoom rectangle, drag and release to indicate the opposite corner. Can be used

on every image.

There are different ways to select the zoom function:

hold down the CTRL key, right-drag your mouse button

right-click in an image or in the 3D view and select Zoom from the context menu

click on the Zoom button in the toolbar

select View > Zoom from the menu bar

Note: The behavior of zooming is different in Reslice Layout.

5. Zoom to fixed factor Allows to Zoom in at a defined factor. Click on the arrow and choose from the drop-down list

the factor you want to zoom with: your cursor becomes a lens.


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6. Zoom to full screen Allows you to display a view on the whole screen. Click on the Zoom to full screen button and

the cursor will change to a magnifying glass. Then click on an image. To return to a normal

view, click again on the Zoom to full screen button.

When you hover with the mouse over a view and click on the spacebar the view is put to full

screen. To unzoom press the spacebar again. You can also zoom to full screen by invoking

the context menu by right-clicking on the view.

7. Unzoom Changes the display scale to show the whole image. You need to select the function first and

then left-click on the view on which you want to apply the function.

Zoom to full screen

on axial view

Zoom to full screen

on axial view

Zoom to full screen

on axial view


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CHAPTER 3: Project Management The project management gives you an overview of all the objects in the project. You can hide

the project menu by toggling the Project Management button in the main toolbar .

The project management consists out of containers which hold a

number of tabs. Each tab stands for a kind of objects in Mimics. It

lists the available objects in the project. On the bottom of a tab

you have a toolbar with the most common functions.

On the toolbar you typically find a create, a delete and a

properties button. The last button on each toolbar is always the

action button . This button lists all the functions that can be

performed on the selected object.

Besides object based tabs there are three different tabs on the

bottom of the project management. The contrast tab allows you

to adjust the gray scale of the images. The volume rendering tab

shows a histogram of the dataset and a line which allows you to

set the opacity of the voxels. The clipping tab lists the possible

clipping planes and their settings.

When the containers are docked in the project management they

have a fixed size. To enlarge them you can undock them by left-

clicking on the pointed top of the container and dragging the

container outside the project management.

The same counts for the different tabs. You can left-click on the

tab and drag the tab outside the container. Tabs can as well be

dragged to another container

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1.1. Masks

A mask is a collection of pixels where all actions (editing, region growing, ..) and calculations

(3D calculations, STL, ..) are based on.

1.1.1. List of the created masks

Name Name of the mask. By clicking on the name of the mask, it can be renamed.

Visible Lists if the mask is visible or not by means of glasses.

Lower Threshold Lower Threshold setting of the mask.

Higher Threshold Higher Threshold setting of the mask.

1.1.2. Functions on masks

New Creates a new mask. On create new mask the threshold bar will pop up,

allowing you to immediately set a threshold or select one of the predefined

thresholds.

Delete Deletes the selected mask

Properties Gives numerical information of the selected mask

Duplicate Duplicates the selected mask

Clear Clears the contents of the selected mask, the threshold of the mask is kept

Calculate 3D Opens the Calculate 3D window

Action Lists the available function on the selected mask

1.1.3. Properties

The mask properties give numerical information about the gray values in the selected mask:


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Threshold low Lower threshold value used for the 3D objects calculation

Threshold high Higher threshold value used for the 3D objects calculation

Minimum value Minimum gray value in the selected mask

Maximum value Maximum gray value in the selected mask

Average value Average gray value from the selected mask

Standard deviation

Number of pixels Amount of pixels in the selected mask

Mask volume The volume of the mask

Scale The scale you are working in: GV (Grayvalues) or HU (Hounsfield Units).

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1.2. 3D objects

1.2.1. List of the created 3D reconstructions

Name Name of the 3D, by clicking on the name of the 3D, it can be renamed.

Visible Lists if the 3D is visible or not by means of glasses.

Contour Visible Lists if the contour of the 3D object is visible on the 2D images or not by

means of glasses. You can change the visibility of the contours by clicking on

the glasses.

Triangles Visible Lists if the triangle edges are visible on the 3D object or not by means of

glasses. You can change the visibility by clicking on the glasses.

Transparency Lists the transparency settings of the 3D, possible options are: opaque (= not

transparent), low, medium and high. Change the transparency by clicking on

the icon in the transparency column. To see your objects transparent, the

transparency button has to be enabled.

Quality Quality which was set before calculation, possible options are: low, medium,

high, optimal, custom.

1.2.2. Functions on 3D reconstructions

New Creates a new 3D. The Calculate 3D window appears.

Copy Copies the 3D to the clipboard. The 3D can then be pasted in another project.

Delete Deletes a 3D object.

Properties Gives the properties of the calculated 3D object.

Duplicate Duplicates the selected 3D model.

Move Activates the handles to move the STL to a new positions

Rotate Activates the handles to rotate the STL around its axis

Action Lists the available functions on the selected 3D object

1.2.3. Properties of a 3D Object

When you click on the Properties button in the 3D Objects list, following dialog box will open:


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Mimics displays the name, color and transparency of the object. The volume, surface, outer

dimensional parameters and the number of points and/or triangles are also shown, which give

a good idea if reducing of the file for further applications is needed.

You can change the transparency of the 3D object and make objects transparent. Drag the

Transparency slider at the bottom of the 3D properties dialog. If the slider is all the way to the

right, the 3D surface is opaque and nothing below the surface can be visualized. If the slider

is all the way to the left, the 3D surface is completely transparent. In order to see the 3D

object transparent, you need to click the Toggle Transparency button in the 3D toolbar.

Opaque 3D Transparent 3D

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If the Details button on the 3D Properties dialog is selected, some measurements of the 3D

object are displayed.

1.2.4. Rotate

When you select a 3D object and click on the Rotate button, rotation handles will appear

around the 3D object.

You can rotate the 3D objects around the selected axes of rotation by grabbing one of the

colored rotation handles. You can also rotate the object around an axis perpendicular to the

camera by grabbing the outer ring of the rotation tool. To change the pivot point, select the

yellow box and move it to its new position.

The orientation of the rotation handles can be altered in the rotation dialog. You can choose

to rotate along the views, inertia or a user defined axis. The user can select to position the

pivot point initially at the center of the bounding box, at the mass center or fixed to a user

defined point.

The rotation value is shown in the status bar.

To rotate in discrete steps, enter an angle in the offset axis field along which you want to

rotate. By clicking Apply you will rotate by the given angle.

1.2.5. Move

When you select a 3D object and click on the Move button, translation arrows appear. To

translate the 3D object grab a translation arrow and move the mouse. To translate the object

parallel to the viewing plane, grab and move the middle of the tool.

You can change the translate axes in the Move dialog. You can choose to translate the object

parallel to the viewing axes, inertia or along a user defined axis.


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The translation value is shown in the status bar.

Translating in discrete steps is possible by entering a reposition measure in one of the offsets

axes. By clicking on Apply you will translate the object by the selected offset.

1.3. Polylines

1.3.1. List of the created Polyline sets

Sets Name of the polyline. By clicking on the name of the polyline, it can be

changed.

Visible Lists if the polyline is visible or not by means of glasses.

Based On Tells on which mask the polylines were calculated. If the set is grown out of

another set, it is independent of a mask.

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1.3.2. Functions on Polyline sets

New Creates a new polyline set. The Calculate Polylines window appears.

Copy Copies the polyline set to the clipboard.

Delete Deletes a polyline set

Duplicate Duplicates the selected polyline set

Color Changes the color of a polyline set

Polyline growing The polyline Growing tool provides the capacity to create several sets of

polylines.

Action Lists the available functions on the select polyline set

1.4. STLs

1.4.1. List of created Objects

Name Name of the object. By clicking on the name of the object, it can be changed.

Visible Lists if the object is visible or not by means of glasses.

Contour Visible Lists if the contour of the object is visible on the 2D slices or not by means of

glasses. You can change the visibility of the contours by clicking on the

glasses.

Triangles Visible Lists if the triangle edges are visible on the 3D object or not by means of

glasses. You can change the visibility by clicking on the glasses.

Transparency Lists the transparency settings of the STL, possible options are: opaque (=

not transparent), low, medium and high. Change the transparency by clicking

on the icon in the transparency column. To see your objects transparent, the

transparency button has to be enabled.

1.4.2. Functions on Objects

Load Loads an STL file into the project.

Copy Copies the STLto the clipboard. The STL can then be pasted in a different

project.

Remove Removes an STL file from the project.

Properties Displays the properties of the selected STL file.


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Duplicate Duplicates the selected STL file.

Export STL Saves the selected STL file (with its current position).

Move When the Move button is enabled, you can move the STL in the 2D views and

the 3D view.

Rotate When the Rotate button is enabled, you can rotate the STL in the 2D views and

the 3D view.

Action Lists the available functions you can perform on the selected STL

Transform Opens the transformation dialog:

In this dialog, you can enter a transformation matrix, invert the transformation

matrix if needed and apply it on the selected STL file.

You can also load a transformation matrix file, written out by Mimics when

reslicing or cropping a project or when doing an STL registration.

1.5. Measurements

1.5.1. List of the created Measurements

Type The type of measure, represented by its corresponding icon. Possible

measures are: a 2D or 3D distance, a 2D or 3D angle, a 2D or 3D diameter or

a density measure. These are the same measures that are available in the

tools toolbar and are represented in the list with the same icon.

Name Name of the measurement.

Visible Lists if the measure is visible or not by means of glasses.

Value Depending on the type of measure this value can represent a distance (mm),

an angle (in degrees) or a mean density (HU or grey values).

Unit Indicates the units corresponding to each measurement value.

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Deviation The deviation in Hounsfield units or grey values for a density measure.

Area The area in mm² of a density measure.

1.5.2. Functions on Measurements

New Shows a menu from where you can choose the type of measure. Possible

measures are: a 2D distance, a 3D distance, a 2D angle, a 3D angle or a

density measure. These are the same measures that are available in the

tools toolbar.

Delete Deletes one or more measures.

Properties Shows the properties of the selected measurement.

Duplicate Duplicates the selected measurement.

Locate Updates all views to show to selected measure. Only angle and distance

measures can be located.

Action Lists the available function on the selected measurements

1.6. Reslice Objects

Online reslice can be performed either along a curve or along a plane. A reslice object allows

you to slice the images in a different direction. To draw a reslice object, select Online Reslice

from the File menu.

The resliced images can only be viewed when the Reslice Layout is chosen in the View

menu.

1.6.1. List of the created reslice objects

Name Name of the reslice object. By clicking on its name, it can be changed. RC

stands to reslice curve, while RP stands to reslice plane.

Visible The active reslice object is indicated by means of glasses. In the Reslice

layout the images corresponding the active reslice object will be shown.

Cross-Section Length

(mm)

The cross-section length determines the width of the cross-section images

when the reslice object is a curve. This length is set to optimal by default, but

can be altered by double-clicking on the Optimal text. This way you can

specify an exact cross-section length.

Note: To return to the Optimal setting after you have specified an exact length, set 0 as the value of the cross-section length.


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1.6.2. Functions on Reslice Objects

New Shows a menu from where you can choose to reslice along a curve or along

a plane.

Delete Deletes one or more reslice objects.

Properties Shows the properties of the selected reslice object.

Duplicate Duplicates the selected reslice object.

1.7. Annotation

1.7.1. List of the created Annotation

Name Name of the annotation. The name is generated automatically based on the

object on which the annotation is attached

Visible The visibility of the annotations is set by means of the sunglasses

Object Lists the object to which the annotation is attached

Text Shows the content of the annotation

1.7.2. Functions on Annotations

New Activates the annotation cursor. Click with your mouse on the object on

which you want to attach an annotation. The annotation properties dialog will

open in where you can add your comments.

Delete Deletes the selected annotation

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Properties Opens the Annotation Properties dialog

Duplicate Duplicates the selected annotation

Locate Updates all views to show to selected annotation.

Action Lists the available actions on the selected annotation

1.8. Contrast

The mapping of pixel values into gray levels is specified by the level and the width of the line

on the histogram. The amount of available gray values levels is dependent on your display

setting. When your display setting is set on true color (24-bit or 32-bit) you will be able to map

the pixel values onto 128 gray levels.

You can change the window by grabbing one of the points or the line and move it with the left

mouse button. You can as well define the position of the points by filling in a value in the

Minimum and Maximum field.

Instead of defining the contrast yourself, you can choose one of the predefined scales from

the dropdown box.

You can change the gray scale also interactively by pointing at an image of interest and

dragging the right mouse button. The cursor will change into . Move the mouse down to

increase the width of the gray scale - this lowers the contrast within the soft tissue. Move the

mouse up to decrease the width of the gray scale - this heightens the contrast within the soft

tissue. Move the mouse to the right to increase the level of the gray scale - this darkens the

soft tissue. Move the mouse to the left to decrease the level of the gray scale - this lightens

the soft tissue. When you are satisfied with your gray scale, release the mouse button. All the

images are updated immediately with the new gray scale.

1.9. Volume rendering

The volume rendering tab shows a histogram of the dataset and a line which allows you to set

the opacity of the voxels. To visualize the volume rendered 3D select the volume render

button in the 3D toolbar. You can find more information about volume rendering in the section

about the 3D toolbar.


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1.10. Clipping

In the clipping tab you can define the different clipping planes and their options. To activate

clipping select the Clipping button in the 3D toolbar. You can find more information about

clipping in the 3D toolbar section


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CHAPTER 4: Shortcut Keys

General Shortcuts

F1 Open the Online Help

CTRL + Z Undo last action

CTRL + Y Redo last action

CTRL + F Enable/Disable the Navigation Toolbar

CTRL + I Makes all mask invisible

CTRL + SHIFT + M Enable/Disable the Movie export

CTRL + SHIFT + Printscreen Copies a screenshot of the active view to the clipboard. From there it can

easily be pasted into another application.

CTRL + SHIFT + P Takes a screenshot of the active view and saves it as Jpeg in the project

folder.

Alt + F4 Exit Mimics

SPACE If you hover with the mouse over a view and press the spacebar; that

view is put to full screen. To unzoom to full screen; press the spacebar

Shortcuts on files

CTRL + O Open a file

CTRL + P Print a file

CTRL + S Save a file

CTRL + N Close a file

Shortcuts on the views

ArrowUp Go to next slice

ArrowDown Go to previous slice

PageUp Go 10 slices up

PageDown Go 10 slices down

CTRL + L Make slice indicators visible/invisible

Right mouse button Adjust gray scale: Move the mouse horizontally while keeping the buttons

pressed to change the level of the gray scale. Move the mouse vertically to

change the width of the gray scale.

SHIFT + Right mouse

button

Pan: Move the mouse while keeping the buttons pressed to pan.

CTRL + Right mouse Zoom: Move the mouse vertically while keeping the buttons pressed to zoom

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button in and out.

Backspace Toggles between zoomed in and unzoom.

Shortcuts on the 3D view

Arrow keys Rotate the 3D view left/right and up/down

Page Up Rotate the 3D view 10 degrees down

Page Down Rotate the 3D view 10 degrees up

Home Rotate the 3D view 10 degrees left

End Rotate the 3D view 10 degrees right

SHIFT + keys above Pan the 3D view

Scroll wheel With the scroll wheel you can zoom in on the 3D view.

ALT + left/right Do washing machine rotation

Shortcuts on the layouts

F2 Image Layout

F3 3D Layout

F4 Reslice Layout

F5 Simulation Layout (if the simulation module is licensed)

Shortcuts on Segmentation functions

Region Growing

CTRL + R Start the Region growing function

Edit

CTRL + E Open the edit toolbar and go in edit mode

While in edit mode:

D Draw

E Erase

T Draw with local threshold

ALT Holding the ALT key switches between Draw and Erase

CTRL + drag left

mouse button

Resize the edit cursor

SHIFT + Left mouse

button

Temporarily release the edit-tool and do 1-click navigation.

Shortcuts on text fields in dialogs

CTRL + C Copy

CTRL + X Cut

CTRL + V Paste


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Shortcuts on Movie Tool

CTRL + SHIFT+ M Start the movie tool

SHIFT+ F8 Start Recording / Stop Recording

SHIFT+ F9 Pause Recording

Shortcuts on Polylines

CTRL + U Update polylines


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CHAPTER 5: CT Gray scale CT images are a pixel map of the linear X-ray attenuation coefficient of tissue. The pixel

values are scaled so that the linear X-ray attenuation coefficient of air equals -1024 and that

of water equals 0. This scale is called the Hounsfield scale after Godfrey Hounsfield, one of

the pioneers in computerized tomography. Using this scale, fat is around -110, muscle is

around 40, trabecular bone is in the range of 100 to 300 and cortical bone extends above

trabecular bone to about 2000.

The pixel values are shown graphically by a set of gray levels that vary linearly from black to

white. Mimics displays the CT images using up to 256 gray levels if your display setting is true

color (24-bit or 32-bit), 128 gray levels if your display setting is 256 color palette, but as few

as 32 gray levels if your display setting is high color (16-bit). The mapping of pixel values into

gray levels is specified by a level and a width. A gray scale is centered about its level.

For example, a level of 0 specifies that water will be displayed as mid-gray. The extent of the

gray scale is specified by its width. The default gray scale used by Mimics allows you to see

the full range of tissue from air in the maxillary sinus to the densest of cortical bone, but subtle

differences in the soft tissue cannot be visualized. If you narrow the gray scale, you can better

visualize subtle differences in the soft tissue or trabecular bone, but at the cost of forcing

cortical bone to be in one gray level: white. Narrowing the gray scale can help you locate the

mandibular canal if it is not easily seen with the default gray scale.

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PART III

Mimics Menus

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CHAPTER 1: File Menu The File menu contains the following items:

You will also find the corresponding buttons in the toolbar.

1. New Project Wizard To start the new project wizard, select New project wizard from the File menu or click on the

icon in the main toolbar. The wizard will start with STEP 1.

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1.1. Selecting images to import

The first step is to choose the source directory of the images to import. You can click

immediately on the drive or folder in the Favorites column or you can browse for the drive or

folder in the File browser.

A folder can be expanded by double clicking or by clicking on the triangle. All images within a

directory are displayed under the folder name. The complete content is shown of the folder.

To select all files in a folder click on any one file and press CTRL+A. To restrict the selection

you can hold down

the CTRL key and left mouse button to select the images one by one

the SHIFT key and left mouse button to select the first and the last image in your

selection

To add a new folder as favorite, select the folder in the File browser and click on Add favorite

button at the bottom of the Favorites column. Right-click on a favorite folder to remove the

folder from the favorites list.

You can force raw import by checking the "Force raw import" checkbox. This allows to enter

manually the parameters of the images as described in the "Reading Raw images" section.

1.1.1. Import log:

The show import log option will give an overview of the files that were detected. This can be

disabled if you do not wish to view the log. The log can be saved as a text file for later

reference by using the Save log button.


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1.2. Importing DICOM images

When you select a set of DICOM images to import, the New Project Wizard takes you to the

following steps.

1.2.1. Selecting studies to convert

In this window information is shown about the studies you are going to convert. In the preview

pane on the bottom you can browse through the images of the selected sequence and check

all relevant header information.

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All studies that are selected will be converted and for those studies, a Mimics file will be made

in the default working folder. To unselect a study, click on the checkmark in front of each

study. Click the Convert button to start the conversion.

If multiple image sequences of the same patient are displayed, this means that not all image

parameters are equal. To merge one or more sequences to one Mimics project, select them

by using the SHIFT key and left mouse button, and click the Merge button . Merging

sequences in not allowed when the patient name, pixel size or image orientation is different.

Mimics also performs a check of the memory needed by the project files along with the

available memory. You can see that at the top of the window. If the available memory is less

than that required, Mimics will give an error and you are requested to free up memory in your

computer, use a different computer, or compress your data.

A description of the different tags and options on this step of the wizard follows:

a. DICOM tags

In the lower right, you can view the information relevant to a particular study. These are

grouped according to following different tags:

i) Acquisition:

This section lists the parameters or scanner settings used to acquire the images.

ii) Critical:

This tab contains parameters that are critical for Mimics to load the images.

iii) Image:

This tab lists out parameters of the imported images.

iv) Main:

These are the main parameters of the DICOM header.


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v) Patient:

This tab contains the patient specific parameters.

b. Grouping

Mimics checks for several parameters during the import of images. If one of these parameters is different, Mimics splits the data set in different parts. You can select or unselect the parameters that you wish Mimics to consider while performing the check, as shown below. The parameters that Mimics checks for are: patient‟s name, phase, protocol name, series description and study description.

c. Compression

There are different types of image compression to choose:

CT: this compression is typically used for the removal of background noise for CT-images.

It is a lossy compression and changes the grayvalue of all the voxels with a grayvalue

between 0 and 200 to 0.

MR: this compression is typically used for the removal of noise for MR-images. It is a

lossy compression and sets the grayvalue of all the voxels with a grayvalue between 0

and 10 to 0.

Cut air: this compression is typically used for the removal of noise for non-calibrated CT

scans such as Cone Beam CT and µ-CT. It is a lossy compression and removes the

grayvalues corresponding to the first peak in the 3D histogram.

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Lossless: when choosing lossless compression, nothing is changed to the voxels of the

images.

Note: if the images being imported are tagged as being CT images, the predefined image compression will be Air cut. Otherwise, Lossless compression will be set by default.

1.2.2. Selecting project to open

Select in this window the set of images that you wish to open in Mimics.

1.3. Reading Tiff, Bitmap and Jpeg images

When you select a set of images in Bitmap, Tiff or Jpeg format an extra window will be

displayed on the screen after clicking Next in the first Import images new project wizard

window. This is the Images Property window. In this Bmp/Tiff/Jpeg Import window you can fill

in some image related parameters and order your images before the conversion is performed.

The radiologist usually provides this information.


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Filenames

The filenames of the image data stack that you wish to import can be seen in on the left.

When you select an image, the up-down arrow buttons become active. These allow you to

position the images in a custom order. You can view the images in the preview as well.

Sorting Order

You can select how the images should be sorted. The available options are numerical

ascending, numerical descending, alphabetical ascending or alphabetical descending orders.

The sort order can be changed interactively by selecting an image in the list and clicking the

Up or Down arrow in the Move box. The image will be moved up or down one position in the

list.

Scan resolution

In the scan resolution section, it is possible to give the resolution of the scan along the x, y

and z directions. It also is possible to indicate in what dimension this resolution is measured

as well from the drop down menu.

When isotropic sampling is checked, the values in x, y and z will be the same as the x value.

Study information

Here you can enter the Patient Name and Institute Name that is relevant to your project.

1.3.1. Edit images

The edit images dialog allows you to crop your images, resample your images and change

the pixel mapping of the images.

a. Volume crop/resize

Here you can crop and resample your images. There are two ways to crop your image:

1. Enter values in the crop dialog box, or

2. Move the bounding box (shown in white) on the 2D image views.

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To resample your data, you can:

1. Scale the data,

2. Change the pixel size, or

3. Skip some images.

Resampling is especially useful if you have a large dataset.

b. Pixel mapping

Here you can map the original grayscale value to a custom range. This allows clubbing

together all pixels above and below your original range to one value and gives you more

values in the regions of interest. This makes it easier to differentiate in between different

materials.

It is also possible map the range of the input grayscale images from 16 bit to 8 bit grayscale

range.


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1.4. Reading Raw images

You can import a Raw images file in the New project wizard by browsing to the file and

clicking Next. The Import log may say that the file is an unknown file, but you can ignore that.

Go ahead and click Next.

Next, the Raw image properties dialog will appear. Here, you need to manually enter the

Scan resolution, Image parameters, and the pixel properties. To add the Study Information is

optional. The options for pixel properties can be chosen from one the drop down options.

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When you click Next, the edit images dialog will appear as in the standard image file import.

1.5. Excluded images

Mimics will detect if the image stack contains images that have the same table position and

automatically exclude them from the project. When this is the case, the following dialog box

will appear to prompt the user.


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2. Open project Open an existing project by selecting File > Open Project from the menu bar or by clicking its

button on the Main Toolbar. When you click on the black arrow on the Open Project button, a

list of previously opened projects appears.

The Open project dialog displays your folders containing Mimics files (*.mcs) on the left side

of the window.

Folders from the floppy-, Compact Disc and zip-drive are also displayed when they are

installed. Click on a folder to see the list of Mimics files in that folder. Use the arrows on the

scroll bar if the patient you wish to view is not displayed. Open a study by clicking once its line

in the list and then the Open button or by double-clicking its line.

There are two different modes in the Open project window. The first mode allows you to easily

browse on your hard disk. The second mode will show you more information for each project.

You can switch between these modes with the button.

Note: The first mode will be disabled when the Hipaa preference, Hide file name is enabled. To change the Hipaa preferences go to Preferences, you can change the Hipaa settings in the General section

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2.1. List of studies

Browse tree Displays the browse tree

Patient Displays the patient name

Study ID Shows the study ID

Study Date Shows the study date

File Displays the file name


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2.2. Functions

Add directory to

Favorites

Adds the current

Make default Makes the selected folder your default

Delete folder To delete the selected folder from the list of favorites.

Browse To select a new directory in order to see the reformatted CT studies the

folder contains. You will be asked if you want to add the folder to the list

of favorites.

Delete study To delete the selected study from your computer.

Search in

Subfolders

Shows all the projects in the folder and subfolders

Switch view Switches between the two browse modes.

Sort by column Quickly sort the studies by a column by clicking on the column header

Change column

order

Change the order of the columns by dragging the column header to the

left or the right

Open Click on the Open button after selecting a study or double-click on a

study to open it

Cancel Closes the Open dialog box

Help Opens the help pages on the Open project subject

2.3. List of favorites

Click on a folder to see the images within the folder. The path of the selected folder is shown

at the top.

Right-click on a folder to display the following context menu.

Rename To change the name of the folder

Remove To remove the folder only from the list of favorites. The folder will not be removed from

your computer.

2.4. Reduce Images

High-resolution images can contain a lot of noise and this means that a noisy 3D is obtained.

When you want to filter the noise within the images or want to speed up the segmentation

functions, use a voxel reduction. The Reduce Images window (see picture) is shown when

loading data sets that require more memory than available or when the preference setting

“Always ask to reduce images when loading” (on the General tab page) is selected. Based on

the amount of images and the pixel size, the necessary amount of memory is calculated and

compared with the total amount of memory (RAM). If more memory is needed than available,

a reduction is proposed.

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This function groups voxels together when loading the study. A reduction value of 1 means no

reduction; every single voxel will be loaded. A reduction of 2 will group 4 voxel together (2 in

the X-direction and 2 in the Y-direction) as 1 voxel with as gray value the mean gray value of

the 4 voxels. The maximum allowed reduction is 5. Since pixels are grouped together, the

noise is filtered out and all segmentation tools work faster.

3. Save project Saves the Mimics project.

4. Save project As Allows you to save the project with another name.

When saving a project that contains 16-bit image information you can choose to save the

projects as a Mimics 14 Project. This will convert the project to a 12-bit project which is

compatible with Mimics 14 and all previous versions of Mimics.

Note: If you chose to save your project as a Mimics 11 Project File, then orientation

information will not be preserved. Thus if an oblique object is saved as Mimics 11 Project,

then it may lead to differences in sizes of 3D objects created from two project files.

When saving the project, you can choose to compress it. The compression algorithm used is

a lossy JPEG compression. Using this option will reduce the size of the project.

You can choose between three different quality presets for the JPEG compression:


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When saving a project, it is possible to compress the images in the project with a lossy JPEG

compression. This way you can reduce the size of your projects. It is possible to choose

between three quality presets:

High Quality – Low Compression

Medium Quality – Medium compression

Low Quality – High compression

The higher the compression factor is, the smaller your files will become, but the worse your

image quality will be.

When you have done a reduction on the images during loading or importing, you can also

choose to keep the reduction when you are saving the project.

5. Close project Closes the Mimics project. If necessary, the program will prompt you to save it.

6. Import STL Loads an STL or an MGX file into the project. It will appear in the Project Management, STL

tab and in the 3D window.

Note: You can only load an STL or an MGX file if a project is open; the function is disabled if no project is opened.

7. STL Library The STL library allows you to create a library with STL files on your hard drive that is easily

accessible from Mimics. The first time you use the STL Library, Mimics will ask where you

want to create this library:

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We recommend creating a new folder on a hard disk with a lot of free space. After you have

selected the directory where the STL library will be located, you will see following interface:

The interface is divided in two parts: the left part will show a directory tree of your library. If

you select an STL in the tree, you will see the properties for that STL in the right part. If you

select a directory in the tree, you will see a list on the right of all the STL‟s that are found in

that directory.


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You can extend the library in two ways:

You can copy STL files in the STL library folder via the Microsoft Explorer. You can also

create new directories or remove files via this way. The changes will be visible the next

time you open the STL library in Mimics or when you click on the Refresh button.

You can create new folders and import STL files in the library by clicking on the

appropriate buttons in the STL library interface.

When you select one or more STL‟s in the tree or in the list on the right and click the Load

button, the selected STL‟s will be loaded in Mimics.

You can also adjust the Name, Manufacturer, Product Line and Description when viewing the

properties of an STL by clicking on the fields. These changes will be saved to a small XML file

in the STL library.

8. Import project

This function allows you to load a Mimics or 3-matic project into the current project, including

3D objects, polylines and primitives.

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Note: You can only load a Mimics or a 3-matic project if a project is already open.

9. Organize images In the organize images interface you can choose which images in your Mimics project should

be visible and used while working with Mimics.

Image List List of images. Here you can select/unselect the images. The red marked


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images will be displayed in the project.

You can easily select e.g. every 2 images with the skip images setting at the

bottom of the window.

Preview Shows a preview of the images if selected. You can set the size of the

preview in the drop down list at the left bottom.

Contrast Displays the current minimum and maximum contrast values for displaying

the images. These minimum and maximum contrast values can be changed

in the adjust grayscale toolbar. You can change the current contrast to the

default for CT or MR images by clicking on the appropriate bullet.

Delete Unselected

images

When marked all unselected images will be removed from the project. This

action cannot be undone.

Add/Remove

Adds or removes images from the project. This can also be done by checking

or un-checking the project column (2nd column) in the Image List or the

images in the grid on the right.

Note: Please be advised that you can lose existing segmentations, measurements etc., when you organize your images.

10. Change orientation If one of the orientation parameters is unknown a window "Change orientation" is displayed

on top of the images. In this last step you need to verify the orientation before you can

proceed.

The orientation parameters are necessary to display the images correctly in Mimics. The

radiologist should provide these orientation parameters, but sometimes this information is

incomplete (in this case there is a red X instead of a string in the orientation windows). The

orientations that Mimics needs to know are the Left-Right, the Anterior-Posterior and the Top-

Bottom orientation.

You will see immediately the result in the images. The orientation strings within the images,

"L", "R", "A", "P", "T" and "B", respectively stand for Left, Right, Anterior, Posterior, Top and

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Bottom. Move the mouse cursor to an 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.

Note that all the other orientation strings are completed automatically.

Note: Please be advised that you can lose existing segmentations, measurements, objects etc., when you change the orientation of your project.

11. Online reslice Using this function you can reslice your project along a specified curve or plane. The curve

consists of a series of points indicated in the axial images, connected by an interpolated line.

The parallel and cross-sectional images are constructed, based on this curve. The plane is

defined based on three points indicated on the 2D images or on the 3D objects.

Select File > Online Reslice from the menu or go to Project Management, Reslice Objects

tab and click on the button called New. If you select Along Curve, the axial view is zoomed to

full screen and the Reslice Curves toolbox will appear on the screen with the second button

already selected. The cursor will change to a pencil and you can indicate the points that

define the curve through which you want to reslice the images.

If Along Plane is selected, the cursor will change to a pencil . After indicating the three

points that define the plane, the Reslice Planes toolbox is displayed, allowing you to rotate,

move and resize the plane.

11.1. Along Curve

Note: STLs are only visible in the parallel images when a straight online reslice curve is drawn.

11.1.1. The Reslice Curves toolbox


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The Reslice Curves toolbox can be accessed via the Reslice Objects tab in the Project

Management. Select the reslice object and click on the Properties button.

a. Label

In this field you can rename the reslice curve.

b. Modify

Click on the Add point button to add a point in the middle of the selected line. When you

hover the mouse above the reslice curve, the cursor will change into a pencil. Click with the

left mouse button to add a point.

In order to exclude a point from the reslice curve click on the point of the reslice curve you

want to delete. The selected point will be colored green. Click then on the Remove point

button.

c. Cross-Section Length

The cross-section length determines the width of the cross-section images. This length is

set to optimal by default, but can you can modify it by selecting the Custom option and

indicating the desired cross-section length in the edit field.

11.1.2. X-Ray image

A yellow border surrounds the X-ray image or parallel view. Its thickness can be set in the

Reslicing menu of the Preference Settings (choose Options > Preferences > Reslicing from

the menu bar).

To display the x-ray view, click on this button , next to the parallel view. To return to the

parallel view, click on this button: .

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11.1.3. Zooming in Reslice Layout

When you left-click once when zooming on a cross-sectional image, that image gets enlarged.

By clicking with the unzoom tool on the enlarged cross-sectional image, you will see the

original view again.

Original View

Zoomed cross-sectional image

11.2. Along Plane


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11.2.1. The Reslice Planes toolbox

a. Label

In this field you can rename the reslice plane.

b. Modify

You can rotate the reslice plane by clicking the Rotate button adjusting the values in the edit

fields or by grabbing the rotation handles to the desired position. By moving the center of the

rotation handles you can move the plane.

When you click on the Resize button, the borders of the reslice plane will be highlighted red

and the mouse cursor will change to a double arrow when you hover over the dots. You

can then grab the edges to the desired position. You can also define the dimensions of the

reslice plane by modifying the edit fields.

12. Reslice Project You can reslice a project by going to the File menu and then choose the Reslice Project

button. Following window will appear:

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Projects can be resliced according to a straight line in any direction. This will create a new

Mimics project on your hard drive. There is an easy-to-use interface available.

The reslice line can easily be drawn in the 2D or 3D views by clicking on the Draw Line

button. The mouse icon will change to a pen and you will be able to draw a straight line in any

of the 2D views by clicking once with the left mouse button to indicate the starting point. To

finish drawing the line, click again with your left mouse button on the ending point of the line.

The bounding box of the new image volume will be shown on the 2D images and in the 3D

view.

The coordinates of the beginning and end point of the reslice line can be adjusted in the edit

fields. You can also rotate the project that will be resliced around the reslice line by adjusting

the rotation angle. Several predefined orientations can be chosen in the orientation dropdown.

Image width, height, pixel size and slice distance can be specified and you immediately get

information about the number of slices that will be in the resliced project. After drawing, you

can still adjust the end points of the reslice line.

When reslicing a project, Mimics will also write out the transformation matrix that was applied

during the reslicing. The file with the transformation matrix will be saved in the folder of the

original project.

13. Crop Project You can crop a project by going to the File menu and then choose the Crop Project button.

Following window will appear:


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The outlines of a box will appear on your 2D views and 3D view. When you apply the

cropping, a new Mimics project will be created for only that part of the dataset in the box. This

way it is possible to create a small project for only the structure you are interested in. Since

the cropped project will contain smaller slices, the speed of Mimics will be increased while

working on the project.

The box can be adjusted by dragging the borders of the box in the 2D views or by adjusting

the box properties in the crop interface.

In the following example, we create a new Mimics project for only the femur, starting from a

dataset that contains the hip.

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When cropping a project, Mimics will write out the transformation matrix that was applied

during the cropping. The file with the transformation matrix will be saved in the folder of the

original project.

14. Make project anonymous This function will save a copy of the project without any patient related information, with the

exception of the age and sex.

15. Project information This window displays the most important project information.

After clicking the edit button you can add or change the dentist name, the clinician name and

some comments.

With the copy button you can copy all the project information in order to paste it in a

document.


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16. Save/print screenshot After selecting the image type on the left of the screen, you will immediately see a preview on

the right. You can select 2 destinations:

To a file: Select Filename in the Destination frame to save the image as a BMP or JPEG

file. A default name will be proposed (patient name + view) and the default folder will be

the folder where the project is stored. You can browse to a new folder by using the yellow

button on the right.

To the printer: select Printer to print the image

To clipboard: copies the image to the clipboard allowing you to paste it into another

application

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The image or the print will show you exactly the same information that is on the screen, so

you will have to prepare your screen with rulers, measurements, etc first before creating the

image or print.

17. Print Allows you to print a standard report showing a General Information page, the axial, coronal,

sagittal images and, after an Online Reslice, the cross-sections and parallel images.


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17.1. Properties

Resolution Resolution of the images

White background Option to print a white background

Dithering Option to print the page dithered or not (halftone) - printer dependent

17.2. Navigation

Display in the Print Preview a specific page of your standard report by clicking the arrow

button and selecting one of the pages out of the list. You can display the next or previous

page by clicking the buttons Next and Prev.

17.3. Print Pages

All pages Print all pages

Current page Print only the page in the print preview

Range Enter the page numbers and/or page ranges (separated by commas) for the

pages that have to be printed. For example 1,3,5-12.

17.4. Functions

Advanced To set some advanced print options.

Edit Info To add comments on the prints.

Print Setup To select the printer

Page Setup To define the page margins and the font. You can also choose the unit: mm

or inch.

Print To start printing

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17.4.1. Edit Info

In this dialog box you are allowed to type some information concerning the study. This

information will be shown in the prints. Open this dialog by clicking the Edit Info button in the

Print window.

17.5. Advanced Printing

In this Advanced Print dialog box you can temporarily overrule some print preferences before

printing. If you prefer another setting permanently, go to Options > Preferences > Printing.

Pages to print Select the pages to print.

Objects to print Select the objects to print.

Distances between

images

Spacing between the cross-sectional images and the parallel images in the

prints. If the cross-sectional spacing in the prints is not the same as in the

images a message will appear about measurements that may not be visible

anymore.

Axial image

The box in the axial image indicates the region of interest. The important

point is the center point of the box and not really the edges. To move the

box, select one of the edges and drag it with your left mouse button.


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Printer info In this window you will find the info about the printer that you have installed.

Use the force color option when you have a color-printer, but when you print

a project, you only get black and white prints. This can happen with e.g.

Codonics printers.

18. List of previously opened files A list of recently processed files is shown in the File menu or when you click on the arrow

next to the folder icon in the toolbar. Click once on the file name to open the study.

19. Exit Will close the Mimics application and will save if necessary.

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CHAPTER 2: Edit Menu

The Edit menu contains the following items:


1. Undo Undo the last action performed. The type of action is mentioned after the word "Undo" in the

Edit menu.

2. Redo Redo the last action you have "Undone". The type of action is mentioned after the word

"Redo" in the Edit menu.

3. Show Undo List A list is displayed with all actions that have been performed. Every action is added to the top

of the list, so the first one on the list is the last action performed.

4. Copy objects to clipboard By selecting this option, you can identify the objects that you want to copy to a second Mimics

or 3-matic project. Objects that can be copied are 3D objects, STL files, polylines and

primitives. The shortcut Ctrl + C can also be used, after indicating the objects from their

respective tab in the Project Management.


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5. Paste objects from clipboard This function allows you to paste the copied objects to your Mimics project. You can also use

the Ctrl + V shortcut.


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CHAPTER 3: View Menu This menu contains the following items.


1. Toolbars Mimics lets you choose which toolbars are visible and which are not.

The toolbars are shown as tabbed toolbars by default. They can be undocked from the main

toolbar by selecting the tab with the left mouse button and dragging it outside the toolbar.

To dock a toolbar back into the main toolbar, select the toolbar bar and drag it over the main

toolbar.

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1.1. Main toolbar

A Main toolbar is displayed underneath the menu. It holds the other toolbars as different tabs.

If the Main toolbar is not displayed, select View > Main toolbar from the menu bar. You can

remove the Main toolbar by selecting View > Main toolbar from the menu bar again. You can

dock the Main toolbar along the top or allow it to float freely anywhere in the image area by

dragging it into place.

1.2. Measurements toolbar

A Measurements toolbar can be activated by one of the tabs next to the main toolbar. If the

Measurements toolbar is not displayed, select View > Measurements toolbar from the menu

bar. You can remove the Tools toolbar by selecting View > Measurements toolbar from the

menu bar again. You can add the Measurements toolbar as a tab to the main toolbar or allow

it to float freely anywhere in the image area by dragging it into place. The Measurements

toolbar displays buttons that are shortcuts to the following menu commands:

Measure a distance

Measure an angle

Measure a diameter

Measure distance over surface

Measure the area and average density within a rectangular region

Measure the area and average density within an elliptical region

Add an annotation to a Mimics object

Draw a profile line

Show 3D histogram

1.3. Segmentation toolbar

A Segmentation toolbar can be activated by one of the tabs next to the main toolbar. If the

Segmentation toolbar is not displayed, select View > Segmentation toolbar from the menu

bar. You can remove the Segmentation toolbar by selecting View > Segmentation toolbar

from the menu bar again. You can dock the Segmentation toolbar in the main toolbar or you

can allow it to float freely anywhere in the image area by dragging it into place. The

Segmentation toolbar displays buttons that are shortcuts to the following menu commands:

Thresholding

Region Growing

Dynamic Region Growing

3D LiveWire

Morphology Operations

Boolean Operations

Cavity Fill


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Edit Masks

Multiple Slice Edit

3D Mask Editing

Smooth Mask

Crop Mask

Calculate Polylines

Update Polylines

Calculate 3D

Label

Cavity Fill from Polylines

Calculate Polylines from 3D

Calculate Mask from object

1.4. Navigation toolbar

A Navigation toolbar can be activated by one of the tabs next to the main toolbar. If the

Navigation toolbar is not displayed, select View > Navigation toolbar from the menu bar.

You can remove the Navigation toolbar by selecting View > Navigation toolbar from the

menu bar again. You can dock the Navigation toolbar as a tab onto the main toolbar or allow

it to float freely anywhere in the image area by dragging it into place.

You can navigate to a certain position in the image dataset by filling in coordinates in the edit

boxes for the Axial, Coronal and Sagittal slice position and by clicking on Apply.

If you change the position of the images by scrolling through the images or by doing a one-

click-navigation, the slice positions in the navigation toolbar will update automatically.

2. Status bar

A status bar is displayed along the bottom of the screen. If the status bar is not displayed,

select View > Status Bar from the menu bar. You can remove the status bar by selecting

View > Status Bar from the menu bar again. The status bar displays the following useful

information:

tips that describe actions taken by tools and menu commands

current gray scale value or Hounsfield unit in the voxel currently pointed at by the cursor

current cursor position in 3D coordinate system

3. Project Management The project Management gives you an overview of the different objects. If the Project

Management is not displayed, select View > Project Management from the menu bar. You

can find more information about the separate tabs in the in the Project Management chapter

in the General Information part.

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4. Project Management tabs You can Show/Hide each tab in the Project Management.

5. Interpolated images This function will allow you to toggle between an interpolated view of the reslices in XZ and

YZ direction

Interpolated Images off

Interpolated Images on

Note: This function will only interpolate the grey value images, the mask will remain the same. Editing on the mask on interpolated images is possible.

6. Show/Hide The following menu is shown:


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Show Volume Rendering make volume rendered 3D objects visible when they are invisible

Hide Volume Rendering make volume rendered 3D objects invisible when they are visible

Show Masks make all masks visible when they are invisible

Hide Masks make all masks invisible when they are visible

Show Measurements make all measurements visible when they are invisible

Hide Measurements make all measurements invisible when they are visible

Show Polylines make all polylines visible when they are invisible

Hide Polylines make all polylines invisible when they are visible

Show Annotations make all annotations visible when they are invisible

Hide annotations make all annotations invisible when they are visible

7. Pan view Every image and 3D object can be panned or moved. When you select the pan function, the

cursor will change to a cross-shaped double arrow. There are different ways to select the pan

function:

Press the scroll wheel and drag the mouse

hold down the SHIFT key, right-drag your mouse button

right-click in an image or in the 3D view and select Pan View from the context menu

click on the Pan View button in the toolbar

hold down the SHIFT key in combination with the arrows-keys for precise rotation

Hold down the SHIFT key in combination with Home / End for quick Left / Right panning

select View > Pan View from the menu bar

8. Rotate view The rotate function is only available on a 3D object. There are different ways to select the

rotate function:








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9. Zoom Allows to Zoom in at a user defined rectangle. Click on the left mouse button to indicate a

corner of the zoom rectangle, drag and release to indicate the opposite corner. Can be used

on every image.

There are different ways to select the zoom function:

hold down the CTRL key, right-drag your mouse button

hold down the CTRL key in combination with the Up / Down arrow keys

hold down the CTRL key in combination with the Page Up / Page Down key

right-click in an image or in the 3D view and select Zoom from the context menu

click on the Zoom button in the toolbar

select View > Zoom from the menu bar

Note: The behavior of zooming is different in Reslice Layout.

10. Unzoom Changes the display scale to show the whole image. You need to select the function first and

then indicate the view on which you want to apply the function.

To quickly toggle between the zoomed-in object and the un-zoomed object, press the

backspace key.

11. Zoom to full screen Allows you to display a view on the whole screen. Click on the Zoom to full screen button

and the cursor will change to a magnifying glass. Then click on an image. To return to a

normal view, click again on the Zoom to full screen button.


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Zoom to

full

screen

on axial

view

When you hover with the mouse over a view and press the spacebar the view is also put to

full screen. To unzoom press the spacebar again.

12. 3D Background color Click View | 3D Background Color from the menu bar to select another background color for

the 3D image.

To set a default color, click Options > Preferences > Color from the menu bar.

13. Toggle gray scale You can quickly toggle between the last two gray scales you selected in one of several ways:

select View > Toggle Gray Scale from the Menu bar or press the Toggle Gray Scale button

on the Main toolbar. The current gray scale's description, level and width will be displayed on

the status bar.

14. Pseudo Colors Mimics provides you with several color scales that can be helpful in viewing the image data.

One gray scale and three pseudo-color scales are provided. The pseudo color scales vary the

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hue (color) and luminance (brightness) within the images. Use color scales to enhance small

differences in the soft tissue or the bone. Unlike the gray scale, the pseudo-color scales are

non-linear. The pseudo-color scales can be used for instance to examine the porosity in

materials.

You can change the scale to one of the pseudo-color scales by selecting View | Pseudo

Color from the menu bar and selecting one of the three color scales from the cascading

menu. To revert back to a gray scale, select Gray from the cascading menu.

14.1. Gray

This is the default gray scale.

14.2. Full Spectrum

The Full Spectrum color scale varies within the standard, continuous range of hues from

orange to yellow to green to blue to red. In order to make air black and bone white, it also

varies in luminance from dark (black) to light (white).

14.3. Sawtooth

The Sawtooth color scale places five discrete hues next to each other. In order to emphasize

differences between tissues of very nearly the same tissue density, the hues are very

different: orange, green, red, blue and yellow. Within each hue, the luminance varies from

dark to light.


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14.4. Triangle

The Triangle color scale places the same five discrete hues next to each other. But, within

each hue (except for yellow, which varies from dark to light), the luminance varies from dark

to light back to dark again.

15. Masks Shade Mimics allows you to change the shades and transparency of the mask. The different settings

are explained below:

Semi All visible masks will be displayed. Only

the active mask will be transparent. All

gray shades from the surrounding tissues

remain visible.

Full All visible masks will be displayed and all

masks will be transparent. All gray shades

from the surrounding tissues remain

visible. Example:

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Active Only the visible masks are displayed. Only

the active mask is transparent, the

surroundings are displayed in black.

Example:

Binary All masks are displayed in binary, the

surrounding background is displayed in

black. Example:

16. Layouts The Layouts list let you easily switch between different layouts. Click on the image below to

see more information about the different layouts.

16.1. Image layout

The Image Layout is the default layout. It shows the axial, coronal and sagittal view in case of

3-panes setting and includes also the 3D view in case of 4 panes. In case of 3-panes setting,

toggling the 3D view will replace the sagittal view. For more information on how to change

between 3-panes and 4-panes setting please look at the Visualization Preferences page.

16.2. 3D layout

The 3D layout shows an axial view and 2 3D views in the 3-panes setting and 3 3D views in

the 4-panes setting.


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In each 3D view, there is a 3D toolbar and each 3D can be manipulated separately.

16.3. Reslice layout

This layout is only enabled after an online reslice. It shows the axial, cross-sectional and

parallel view. In case of 3-panes setting, toggling the 3D view will replace your axial view.

17. Toggle 3D Window To view the 3D pane in the Mimics work area in 3-panes setting, click on the 3D button on the

Main Toolbar. The sagittal view will be replaced with the 3D view and a 3D toolbar.

You can also work in 4-panes setting, in which case you see all image views and a 3D view.

In that case, the Toggle 3D button is not present.

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If you have not yet created a 3D, you can calculate a 3D by selecting this button in the

Segmentation toolbar: . The 3D objects list dialog will be shown, listing all 3D objects.

Click the Options button to adjust 3D generation parameters to your needs. Then click the

Calculate button to start calculating the 3D. The 3D is automatically shown on your screen

after calculation.

18. Alignment image You can view the alignment image by selecting View > Alignment Image from the menu bar

or by clicking the Alignment Image button on the Main Toolbar. The alignment image (also

called a Localizer, ScoutView, Pilot, Scanogram, Topogram, or Surview depending on the CT

manufacturer) is a lateral X-ray-like view of the patient. Inspect the alignment image to check

that your patient was positioned correctly for the CT scan. Left clicking in the alignment image

allows you to navigate in all images.

The alignment image is surrounded by a frame border. The H and F markers show you the

direction toward the patient‟s head and feet. Notice the red vertical line. It references the

exact location of the axial image. The dashed red lines reference the first and last axial

images and show the extent of the area that was scanned.

You can move the alignment image anywhere on the screen by dragging its title bar. To

remove the alignment image, select View > Alignment Image from the menu bar, click the

Alignment Image button on the Main Toolbar, or click its Close icon.

Note: Be aware that the Alignment Image will display incorrect information, when using a wrong orientation for a project. You can find more information about changing the orientation on the Change Orientation help page.

Toggle 3DToggle 3DToggle 3D


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CHAPTER 4: Measurements Menu The Measurements menu contains the following items:


1. Measure distance This tool allows you to measure distances within the images and on 3D models. Select the

measurement icon from the Measurements toolbar or select Measurements > Measure

distance from the menu. The cursor will change in a measuring rule. Click once the left

mouse button to set the first point. A measurement will be shown together with its length

(expressed in mm). Click again to fix the other end of the measurement. Fine adjustments can

be made to the measurement by dragging either end to a new location.

To show its context menu, right-click on the measurement.

Delete Delete the measurement

Hide Hide the measurement

Measurements... Activate the measurements tab in the Project Management

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2. Measure angle This tool allows you to measure angles within the CT images, the alignment image and on 3D

models. Select the angle icon from the Measurements toolbar or select Measurements >

Measure angle from the menu. The cursor will change to a measuring instrument. Click three

points with the left mouse button to define the angle. The angle is expressed in degrees and

shown on the screen. Fine adjustments can be made to the angle by dragging the center

point or one of the ends to a new location.

To show its context menu, right-click on the angle.

3. Measure diameter This tool allows you to measure diameters within the CT images and the 3D objects. Select

the diameter icon from the Measurements toolbar or select Measurements > Measure

diameter from the menu. The cursor will change to a measuring instrument. Click three points

with the left mouse button in the contour of the structure for which you want to measure the

diameter. The diameter is expressed in millimeters and shown on the screen. Fine

adjustments can be made by dragging one of the points to a new location.

To show its context menu, right-click on the diameter.

4. Shortest distance over surface This tool is designed to measure the shortest distance over the surface of a 3D model. To use

this tool go to Measurements > Measure distance over surface or select the icon from

the Measurements toolbar. The tool will change into a pencil. Indicate several points that

indicate the path you want the measurement to follow. The measurement is expressed in mm


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and shown on the screen. Fine adjustments can be made to the measurement by dragging

one of the points to a new location.

To show its context menu, right-click on one of the end points.

5. Measure density in rectangle This tool allows you to measure the area and average density within a rectangular region.

Select the rectangle icon from the tools toolbar or select Tools > Measure density in

rectangle from the menu. Move the rectangle to the image you want to measure. Click to

drop the rectangle on the image. Or, drag with the left mouse button to drop the box and

change its size in one step. The rectangle expands and contracts as you move the mouse.

Release the mouse button when you are satisfied with the size of the rectangle.

Information appears about the area (mm²), the mean density (Hounsfield Units or Gray

Values) and the standard deviation of the density (Hounsfield Units or Gray Values) within the

rectangle. You can adjust the size of the rectangle by dragging a border or corner when the

cursor changes to a white double arrow. To move the rectangle, place the cursor on a yellow

border (the cursor changes to a hand) and drag it. The measurement data is recalculated

when you release the mouse button.

When you scroll through the images, the measurements are updated.

To show its context menu, right-click on the rectangle.

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Delete Delete the rectangle

Hide Hide the rectangle

Measurements List... Activate the measurements tab in the Project Management

6. Measure density in ellipse This tool allows you to measure the area and average density, within an elliptical region.

Select the ellipse icon from the tools toolbar or select Tools > Measure density in ellipse

from the menu. Move the ellipse to the image you want to measure. Click to drop the ellipse

on the image. Or, drag the left mouse button to drop the ellipse and change its size in one

step. The ellipse expands and contracts as you move the mouse.

When you release the mouse button, the area (mm²), the density (Hounsfield Units or Gray

Values) and the standard deviation of the density (Hounsfield Units or Gray Values) within the

elliptical region is displayed. You can adjust the size and shape of the ellipse by dragging one

of the four markers on the ellipse when the cursor changes to a double arrow. To move the

ellipse, place the cursor on a non-marker portion of the yellow border (the cursor changes in a

hand) and drag it. When you release the mouse button, the new measurement data is

displayed.

When you scroll through the images, the measurements are updated.

To show its context menu, right-click on the ellipse.

Delete Delete the ellipse

Hide Hide the ellipse

Measurements List... Activate the measurements tab in the Project Management

7. Add Text Annotations

You can add text comments using the annotation tool . Select the annotation tool and

indicate the structure on which you want to comment. You can indicate structures on the

images or on the objects in both, 2D and 3D views. Selected the annotation tool and left click

your mouse, the Annotation Properties dialog will pop up. You can now add your comments

in the text field.


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Arrow Style Style of the line ending

Text Rotation Direction of the text

Text alignment Alignment of the test

Text Comments that will be shown in the project

Note: When you add a long text as comment, it will be visualized as three little dots. The full text is shown when you hover over the annotation. When you double-click the text comment, you can edit it.

To show the annotation context menu, right-click on the annotation.

Delete Deletes the text annotation

Hide Hides the text annotation

Properties Opens annotation properties dialog

Annotation List Brings the annotation tab in the project management to the front

8. Profile line Visualizes an intensity profile of the HU or Gray Values along a user defined line. To draw this

line, click the left mouse button to indicate the starting point of the profile line, move the

mouse to the end position of the line and click again. The Profile dialog graph will be

displayed:

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8.1. Figure

In the figure you can see the intensities for each point along the created profile line. The

minimum and maximum threshold you want to apply can be changed by moving the

horizontal lines.

8.2. List of profile lines

Profile Profile name of the profile line. Click on its name to change it (similar as in

Windows Explorer).

Visible Shows by means of glasses if the profile line is visible or invisible in the

images. Left-click on the glasses to toggle between visible/invisible.

8.3. Functions on profile lines

Locate Updates the 2D view to show the position of the profile line.

Color Allows you to change the color of the selected profile lines.

Delete Deletes the selected profile lines.

End / Start Thresholding By Clicking this button, this dialog box will be closed/ opened and the

threshold will be applied in your images.

8.4. Options

Scale to fit Allows you to see the vertical axis with all Hounsfield values or only the

values lower than the maximum value along the profile line.

Grid X-axis To show or hide the vertical grid lines.

Grid Y-axis To show or hide the horizontal grid lines.

8.5. Measuring

There are three measurement methods:


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4 point method (suggested for technical parts): The user will see four full lines numbered

from 1 to 4, each with a different color. The full lines represent the input. The software

calculates the intersection point of the vertical lines with the profile line: four points are

calculated. The corresponding HU values can be read by following the full horizontal lines.

On each side of the peak, a point is calculated as follows: P1 is at the position of the

profile line where the HU value equals “T(gvalue2-gvalue1)+gvalue1” and lies between

line1 and line2 on the horizontal axis. The dashed white lines indicate this point. The “T”

function in above expression is the percentage of threshold difference. Most of the time

this is about 50%. P2 is calculated in a similar way but with lines 3 and 4 as parameters.

This point is indicated by the dashed yellow lines. The distance between P1 and P2 is the

requested dimension.

4 interval method (suggested for technical parts): Instead of indicating 4 points, the user

will indicate 4 intervals. For each interval the average value is calculated. These four

average values will then take over the role of the 4 points as described in the 4 point

method.

Threshold method (suggested for medical images): Start the thresholding and drag the

threshold line to the right position. Click on the End Thresholding button. The yellow and

white dotted lines will move to the intersection between the profile line and the threshold

line. The distance between the lines is displayed in mm.

The 4 point method and the 4 interval method are suggested for technical CT images, while

the threshold method is suggested for medical applications.

In case you choose the 4 point method or 4 interval method, you will also see two horizontal

lines (yellow and white). They indicate the position of the threshold value following the

percentage filled out in the dialog box.

The measurements are shown in the images and are saved to the project. They are also

listed in the Measurements tab page of the project management. Like this you can always

refer to the measurements made and pop-up exactly the same profile line as initially created.

9. 3D Histogram The 3D Histogram is the histogram of the complete data set. The X-axis lists the HU or

Grayvalues, along the Y-axis the number of pixels that have this value. The range of this axis

can be user defined or automatic (all values). The Y-range can be logarithmic or decimal. To

activate the changing of these settings, you need to click on the Update button.

The histogram function can be saved as a text file which can be easily imported in other

programs.

Note: The Grayvalue 0 (-1024 HU) is not included in the histogram, since for most data sets, the number of pixels for that value is much higher than for other values, resulting in a non-optimal view of the rest of the histogram.


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CHAPTER 5: Filter Menu This menu contains the following items:

Image processing is commonly used to enhance low quality images, by performing high

degree noise reduction. Therefore, digital filters can improve higher-level processing steps,

such as segmentation.

1. Binomial blur Blurring filters are traditionally used to remove noise from images, by attenuating high spatial

frequencies. The Binomial blur filter computes a nearest neighbor average along each

dimension. You can specify the number of times you want to repeat the process.

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2. Curvature flow The Curvature flow filter performs an edge-preserving smoothing on the images. The iso-

contours of the images are viewed as level sets, where the pixels with a particular grayvalue

form one level set. The diffusion speed is proportional to the curvature of the contours.

Therefore, areas of high curvature will diffuse faster than areas with low curvature. Hence,

small jagged noise artifacts disappear quickly, while large scale artifacts evolve slowly,

thereby preserving sharp boundaries between objects.

You can specify two parameters: the number of iterations to be performed and the time step

used in the computation of the level set evolution. The typical value for the time step in is

0.125. The number of iterations can usually be around 10.

3. Discrete Gaussian The Discrete Gaussian filter computes the convolution of the image with a Gaussian kernel

for calculating the transformation to apply to each voxel. You can specify a value for the

variance associated with the Gaussian kernel and also the maximum kernel size. This filter is

used typically to smooth and reduce the image detail, preserving the edges for low variances.


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4. Gradient magnitude The magnitude of the image gradient is extensively used in image analysis, mainly to help in

the determination of object contours and the separation of homogenous regions. The gradient

magnitude filter computes the magnitude of the image gradient at each pixel location. This

filter does not apply any smoothing to the image before computing the gradients. The results

can, therefore, be sensitive to noise.

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5. Mean The mean filter is commonly used for simple image noise reduction. Each output pixel is

computed by finding the statistical mean of the gray-level values surrounding the

corresponding input pixel. Note that this filter is sensitive to the presence of outliers in the

neighborhood and does not preserve the image edges.

You can set the size of the neighborhood over which the mean is computed.


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6. Median The median filter is particularly useful to reduce speckle noise and salt and pepper noise. Its

edge-preserve nature makes it useful in cases where edge blurring is undesirable. This filter

computes the value of each output pixel as the statistical median of the neighborhood of

values around the corresponding input pixel.

You can set the size of the neighborhood over which the median is computed.

7. Show filtered images By selecting or unselecting Show filtered images, you can switch between the view before

and after applying the filters.

Show filtered images off Show filtered images on

Note: If you reselect Show filtered images, the filtering operations will be reapplied to the imageset. This operation may take a few minutes.

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8. Edit filter list In the list of filters you can add, edit or remove the filters that have been applied to the

imageset.

New Creates a new filter.

Delete Deletes a filter.

Move Up / Down Reorganizes the order of the filters.

Help Opens the Help pages under the Edit filter list

Note: When the order of the filters is altered, these filters will be reapplied to the imageset. This operation may take a few minutes.


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CHAPTER 6: Segmentation Menu This menu contains the following items:


1. Thresholding There are two ways of thresholding:

1.1. With the thresholding toolbar

Set the threshold of the active mask. You can set or change the active mask in the Masks tab

of the project management.

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Thresholding is used to create a first definition of the segmentation object. The object can be

defined based on one lower threshold, or based on a lower and a higher threshold. In the

former case, the segmentation object will contain all pixels in the images with a value higher

than or equal to the threshold value. In the latter case, the pixel value must be in between

both threshold values to be part of the segmentation object.

The predefined threshold allows you to quickly select a threshold for a specific tissue type.

The threshold can still be adapted to your needs.

The threshold value can be changed by moving the sliders in the thresholding toolbar with

real time visual feedback. The threshold value will be displayed in the threshold toolbar and

the segmentation area is changed accordingly.

With the two sliders a minimal and a maximal threshold can be set. (Mostly only the minimal

value needs to be set) In the Min and Max box, a threshold value can be filled in or the value

can be increased or decreased using the up-down controls (ideal for fine tuning the

threshold).To accept these values, click Enter.

Note: The upper and lower threshold limit is limited to the maximum and minimum intensity in the project.

To use the threshold, press the Apply button.

1.2. With a Profile Line

To use a profile line for thresholding, select the Profile line button from the tools toolbar.

To draw the line, click the left mouse button to indicate the starting point of the profile line.

Then, click the left mouse button again to determine the end point of this line. Now you can

use the measurements made with the profile line to determine the lower and upper threshold

values.

When Start Thresholding is enabled on the Profile Line dialog box, you can easily change

the lower and upper threshold values by grabbing and moving the green lines. These lines

represent the lower and upper threshold values.

You can find more information about profile lines on the Profile Line help page.


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2. Region Growing

The Region Growing tool provides the capacity to split the segmentation into separate objects.

The operation can be performed on one single slice (multiple layer is Off) or in 3D on all slices

(Multiple layer is On): to do this, turn Multiple Layer On or Off in the Region Growing

Properties toolbar.

Source and target masks are set here. The target mask can be a new mask or an existing

object, in which case the selected region will be added to this object.

After entering the appropriate values, click the left mouse button (cross shaped) on one point

of the object of interest (which has to be part of the current segmentation object.). All points in

the current segmentation object that are connected to the marked point will be moved to the

target mask.

If two existing masks are chosen in the source and target box, the double arrow can be used

to switch source and target.

When the check "Leave Original mask" is marked, all selected information will be copied and

pasted in the new mask. When it is turned off, all selected information will be removed from

the source mask and placed in the target mask (compare it to cut and paste).

3. Dynamic Region Growing

The Dynamic Region Growing tool allows you to segment an object based on the connectivity

of gray values in a certain gray value range. It allows an easy segmentation of blood vessels,

nerves, ... in CT images.

The Dynamic Region Growing function is the only operation where you don‟t have to

threshold. A threshold value will be set automatically, the minimum and maximum value of the

created mask will serve as threshold values.

The creation of this new mask starts when you select a pixel. Mimics starts comparing the

gray values of the neighboring pixels. The pixels with gray values that obey the following rule

will be added to the new mask.

|î -i | < d with

î the average gray value

i the new gray value

d the deviation.

If you make a second mouse click while holding down the CTRL key on your keyboard,

above rule will also be applied on the gray value of the selected pixel.

Target The new mask that will be created or if you select an existing mask, Mimics will

take into account the gray values of the pixels that are already in this mask.

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Fill Cavities This feature enables filling internal gaps of the selected mask and places this in

a new mask or in an existing one.

Multiple Layer When this is marked, Mimics will look in the complete data set. When it is

unmarked, the function will only be applied on the single slice.

Seed point Shows the Hounsfield/Grayvalue of the last selected seed point.

Deviation Min and max indicate the deviation range from the seed point.

Note: The deviation parameter in previous versions of Mimics was expressed with 1 byte (0-255), while from Mimics 8.0 the complete grayvalue range of 12 bits (0-4095) is used so the deviation can be better fine-tuned. This means that you have to use a deviation that is much higher than in Mimics 7.3 to get the same results.

Example:

Selection of the alveolar nerve with one mouse click:

2D

3D

4. 3D LiveWire The 3D LiveWire tool is an interactive segmentation method in which you indicate some

points lying at the boundaries of an object. Based on this information, a 3D mask is created

following the exact object contours. This function is particularly suitable for MR and low

contrast images.

The first step is to choose the orientation of the automatic segmentation. If you select the Axial view, this means that you will indicate the points lying in the border of your object in the Coronal and Sagittal views. Indicate several points around the structure you want to select. A line is drawn between the points and snaps to the boundaries of the object. Depending on the image gradient, the snapping will be more or less accurate. You can adjust the parameters in the tool dialog – Gradient Magnitude and Attraction – or you can draw straight lines by pressing the Ctrl key and moving your mouse. The parameters in the dialog can be applied to all the contours in the dataset - by selecting the checkbox Apply parameters to all contours -, or to a range - by clicking on the Start button. To close the contour, you just need to double-click on the corresponding view. You can delete one contour by right-clicking on the slice where the contour was drawn and selecting


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Delete all contours on current slice. The same can be done for all the contours drawn in that view.

Repeat the procedure for several slices in the Sagittal and Coronal views. Obviously, the higher the number of contours indicated, the more accurate the segmentation will be.

Each contour is displayed in the automatic orientation view as a (turtle) line. The automatic calculation of the contours in the Axial view can be fine-tuned by dragging the dots to the correct position, or by drawing new lines to constraint the position of the contours. Each line of the turtle map has to intersect at least one line. Lines without any intersections will not be used for the segmentation process. You can also delete construction lines by right-clicking on top of the selected line and selecting Delete construction line.

The same can be done for all the construction lines in one slice or in the complete dataset.

Note: Keep in mind that when you add constraint lines, the final contour will only be adjusted in the slice where the constraint was inserted.

You can change the orientation for automatic

segmentation and estimate the view of the turtle

maps on the other orientations.

Once the contour in the Automatic contour view follows the correct contours of the structure to be segmented, click on the Segment button. A mask will be created and added to the masks list in the Project Management. After generating the mask, you can still adjust the

contours and control points. Simply choose you mask,

select the LiveWire tool and move the control points to

the desired position or adjust the turtle lines.

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4.1. The 3D LiveWire Interface

Target The mask that will be created when applying the 3D LiveWire tool

Automatic contour View for which the automatic contour will be generated, based on the

points selected on the boundaries of the object in the two other views,

and that will lead to the calculation of the mask.

Apply parameters to all contours If this option is ON, the parameters selected for Gradient magnitude

and Attraction will be applied to all the automatically calculated

contours. If this option is OFF, the parameters will be applied only for

the automatically calculated contour present in the slice displayed in

the screen.

Gradient magnitude This parameter indicates to which kind of gradients the contour will be

attracted. If the selected value is close to 0%, the contour will be

attracted to darker regions on the boundaries of the object. If the

selected value is close to 100%, the contour will be attracted to

brighter regions lying at the boundary of the object/

Attraction The attraction coefficient indicates if some cavities in the boundaries

of the object should be taken into account or should be neglected. If a

value near to -3 is selected, all the small inclusions will be included in

the mask. If a value near to 3 is selected, the inclusions will be

excluded from the automatic contour.

Apply parameters to range This option allows applying the selected parameters to a range of

slices in the dataset. When you click on the Start button, you indicate

the first slice of the range. Scroll then through the dataset, until the

last slice to which the parameters should be applied and click on the

Stop button.

Segment When you click on the Segment button, a mask is calculated based

on the automatic contour.

5. Morphology Operations

Morphology Operations will perform actions on the 'form' of a mask. The different morphology

operations are:

Erode

Dilate


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Open

Close

All these functions will take or add pixels from the source mask, the result will be copied in the

target mask.

Source The Source mask is the mask that will be altered.

Operation Erode: erode will take pixels from the edges. Erode followed by a region

grow can separate parts.

Dilate: dilate will add pixels from the edges. This can be used to restore the

effect of the erosion. You can limit the effect of dilation to another mask. This

is to prevent that you will have an end-result that is larger than wanted.

Open: will perform first an erosion, immediately followed by a dilation. Small

edges will be removed or opened.

Close: will perform first a dilation, immediately followed by an erosion. Small

cavities will be closed.

Target The new mask that will be created.

Limited to : You can limit the effect of an operation to another mask. This is to prevent

that you will have an end-result that is larger/smaller than wanted.

Number of pixels is the amount of pixels you will take/add in one operation

8-connectivity

26-connectivity

8- connectivity 26-connectivity

8-connectivity will only look at the neighboring pixels in the plane. (The

operation is performed on the complete dataset)

26-connectivity will look at the neighboring pixels in 3D. However, to take

effect, the slice distance must be equal or less than the size defined by the

number of pixels (pixel size * number of pixels).

The lower and upper threshold boundaries of the target mask will be taken over from the

source mask

After entering the appropriate values, click the Apply button.

6. Boolean Operations

The Boolean operations allow you to make all different kinds of combinations based on two

masks. It is a very useful tool to reduce the work that needs to be done when separating two

joints.

After entering the appropriate masks and operation, click on the Apply button.

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The threshold limits of the resulting mask will be updated according to the values of the

masks A and B and the operation applied:

Subtraction (Minus):

Threshold value = Threshold value mask A

Intersection:

lower threshold = max (low mask A, low mask B))

higher threshold = min (high mask A, high mask B))

Union:

lower threshold = min (low mask A, low mask B))

higher threshold = max (high mask A, high mask B))

Example: Separation of a knee joint

The image with the green mask is the starting situation. As you see the tibia and femur are

connected with each other.

So some erasing is necessary. The result is shown in the cyan mask. You only have to edit

one part. Then region grow it e.g. to the purple mask. Now you can subtract the purple mask

with the first structure from the cyan mask that contains both structures and you immediately

have the second structure (red mask).

7. Cavity Fill Fills internal gaps of the selected mask and places this in a new mask.

Source and target masks are set here. The multiple layer checkbox indicates if you will fill in

3D or just in 2D.

Select the cavity to fill by a click of the left mouse button (bucket shaped).

Please save your project first before performing the Cavity Fill. The Cavity Fill function might

lead to surprising results when there is a "gap" to the surrounding area. Therefore, it is best to

take a new mask to fill the cavity in.

Below is a trick to fill a lot of internal holes at once:


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8. Edit Masks All manual editing functions are performed on the active mask. You can draw, erase, or

restore the image with a certain threshold value indicated below. The drawing cursor can be a

rectangle or a circle (ellipse) and can have different sizes, or you can use the lasso tool to

draw a shape.

Below the following bar appears:

Type Shape of the edit cursor: square (rectangle), circle (ellipse) or the Lasso and

the Flood-fill and the LiveWire tools.

To use the Lasso tool: select Lasso as Type, then draw with your mouse on a

slice while pressing the left mouse button. To end the drawing, release the

left mouse button.

To use the Flood-Fill tool: select Flood-Fill as Type, select a point in the area

you are interested in selecting and move you mouse keeping the left button

pressed. The selected area grows until an edge in the image is detected.

To use the LiveWire tool: select the LiveWire as Type and indicate

some points at the boundaries of the part you want to select. A line is

created between the points and snaps to the contours of the object.

The line indicates the region where the selected operation will be

applied.

Width/Height Size of the edit cursor (can be different if the Same Width and Height check

box is switched off).

The size can be adjusted interactively by keeping the CTRL button and the

left mouse button down, when you move the mouse now, the size will

change.

Tolerance/Impatience The tolerance controls the edge detection in the image, in order to stop the

contour from growing outside the limits. The higher the value, the sharper the

image edge has to be to stop the contour growth. The impatience represents

the speed of expansion out of current region. When the contour approaches

an edge, the speed of expansion will gradually decrease.

Draw Draws in the active mask

Erase Erases in the active mask. To erase a full slice right-click in a view and select

“erase full slice” from the context menu.

Threshold Changes the edited zone back to a local threshold value which is set on the

right side. When the default values are used, areas where some drawing or

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erasing has been done can be restored to their original threshold. This local

threshold tool can be used to remove artifacts in the images, to restore the

original threshold after you draw or erased some pixels by mistake…

There are 3 threshold ranges. The middle threshold range is the default

threshold that is currently applied to the active mask. This default threshold

cannot be changed. To use your own threshold range, click on the arrow keys

(up or down), double click on a threshold value, change the value and press

enter.

When you move the edit cursor (square/circle/outline) over an image while

pressing the left mouse button, every pixel within the square/circle/outline and

which has a threshold within the threshold range you set, will be added to the

active mask. On the other hand, all the pixels that already belong to the

active mask and which don‟t have a gray value within the range will be

removed from the mask.

Note: This threshold is a local threshold, meaning that you apply a threshold in a particular area of one image and not on the other images in the project. You need to repeat the local threshold action on each image that is needed. The difference with the threshold function in the Segmentation menu is that the one from the segmentation menu is a global threshold that applies to every image in the data set.

After editing, pressing this button will update the polyline in the current image.

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.

9. Multiple slice edit The multiple slice edit tool is great to remove scatter easily. It allows you to reuse the manual

editing that you have done on one slice, on other slices. The multiple slice edit works by

creating a temporary mask that can be edited. The active voxels of the temporary mask are

then added or removed from the original mask or a local threshold is done on the original

mask at the active voxels.

In the interface, first choose which slices you want to edit (Axial, Coronal or Sagittal). You will

notice that all masks are hidden except the active mask. Then choose to draw on the selected

view and you will notice that a new temporary mask is created automatically with a different

color.

You can draw or erase pixels from the temporary mask and copy the current slice of the

temporary mask on the current slice to other slices. The intersecting parts of the temporary

and active mask are colored in a third color. To copy the temporary mask of the current slice

to other slices, adjust the number of slices the current slice will be copied to and click on one

of the arrow buttons. If you choose to copy to 0 slices, the current slice will be copied to all

slices above or below the current slice.

You can still adjust the temporary mask on the other slices and then use this new result again

for copying to other slices. Finally, the temporary mask is removed or added from or to the


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active mask or a local thresholding operation is done on the active mask at all the active

voxels of the temporary mask.

The original mask.

Remove the scatter by selecting the scatter on the

temporary mask. In this example, the temporary mask

has a purple color and the intersecting parts of the

temporary and active mask, have a yellow color.

Remove the pixels in the temporary mask from the

original mask.

9.1. The multiple slice edit interface

Type Shape of the edit cursor: square (rectangle), circle (ellipse) or the Lasso and

Flood-Fill tools. To use the Lasso tool: select Lasso as Type, then draw with

your mouse on a slice while pressing the left mouse button. To end the

drawing, release the left mouse button.

To use the Flood-Fill tool: select Flood-Fill as Type, select a point in the area

you are interested in selecting and move you mouse keeping the left mouse

button pressed. The selected area grows until an edge in the image is

detected

You can also create a mask here by choosing the LiveWire option to better

define anatomical structures.

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box is switched off).

The size can be adjusted interactively by keeping the CTRL button and the

left mouse button down, when you move the mouse now, the size will

change.

Tolerance/Impatience The tolerance controls the edge detection in the image, in order to stop the

contour from growing outside the limits. The higher the value, the sharper the

image edge has to be to stop the contour growth. The impatience represents

the speed of expansion out of current region. When the contour approaches

an edge, the speed of expansion will gradually decrease.

Select Adds to the temporary mask. To select a full slice right-click in the slice and

select “select full slice”.

Deselect Deselects from the temporary mask.

Copy to slices Determines on which view you can edit the temporary mask and in which

view the mask will be copied to the other slices. You can choose between

Axial, Coronal and Sagittal.

Number of slices To which slices you want to copy the temporary mask of the current slice. If

you set the number of slices to 0 you will copy the current slice to all slices

before or after the current slice.

If you set a value different from 0, you will immediately jump to the last slice

where the temporary slice is copied to.

Interpolates the temporary mask between different slices.The interpolation is

applied according to the selected view (Axial, Coronal and Sagittal) in Copy

to slices.

Only after applying previous interpolation you can do next interpolation for

other selected regions.

Operation on the

active mask

Determines the operation that will be done on the active mask. You can

choose to remove the voxels in the temporary mask from the active mask,

add the voxels in the temporary mask to the active mask or do a local

thresholding on the voxels of the active mask, where the voxels of the

temporary mask are active.

10. Edit Mask in 3D The 3D mask editing tool allows you to visualize and edit the mask in 3D. A 3D preview of the

mask is showing. On this 3D preview you can indicate a region. The pixels that correspond

with this selection can removed from the mask or separated into a new mask. This tool is very

helpful when removing scatter and for separating complex structures like vessels or fractured

bones.

The tool works with a region of interest that can be moved and rescaled in the 2D views. The

region of interest is needed to make sure rendering is fast enough. You can change the size

of the ROI in the Mask tab of the preferences in case you pc is too slow for the default option.


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3D preview of the mask Selection of the region to edit Selected region

Type Shape of the edit cursor: square (rectangle), circle (ellipse) or the Lasso tool.

To use the Lasso tool: select Lasso as Type, and then draw with your mouse

over the 3D preview while pressing the left mouse button.


box is switched off). The size can be adjusted interactively by keeping the

CTRL button and the left mouse button down, when you move the mouse

now, the size will change.

Select Adds the indicated region to your selection

Deselect Removes the indicated region from your selection

Grow The grow tool only selects the 3D model on which you applied the tool,

discarding all loose parts.

Invert Inverts the current selection.

Hide Hides the current selection

Show Showed the hidden selection

Removes Removes the current selection from the mask

Separate Moves the selection into a new mask

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11. Smooth Mask The mask smoothing tool filters outliners resulting from manual segmentation, while

preserving important boundaries. By applying this operation, existing artifacts in the active

mask are removed and consequently the surface quality of the calculated 3D objects is

improved.

Before mask smoothing After mask smoothing

12. Crop Mask The mask cropping tool allows you to easily select a region of interest and restrict your

segmentation to that region of interest. When cropping a mask, everything outside region of

interest will be removed from the mask. The difference with the Crop project tool is that even

though you restrict your mask, the images in the project remain untouched.


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13. Calculate Polylines The calculated polylines are the high resolution segmentation contours for the current

segmentation object identical to how they will be calculated by STL+. It can be used to

determine the exact threshold value(s) for a correct segmentation. Pressing the Calculate

polylines button results in the following window:

To start calculation, select the desired masks and click Calculate.

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If your selection contains a polyline that has a deformed shape, update that polyline in the

following way:

Select the Edit tool .

Alter your segmentation mask with the draw or erase function.

Click the Update button or select Update polylines from the Segmentation menu.

Repeat this in every slice where the polylines need to be updated. If polylines need to be

updated in a lot of slices you better alter first your segmentation mask in every slice and then

recalculate the polylines for the whole mask.

14. Update Polylines After changing the segmentation on one layer, the current polyline can be updated by clicking

this button.

Note: When the threshold value has changed, the complete set of polylines needs to be calculated again.

15. Calculate 3D Click on Calculate 3D from the Segmentation Menu, on the Calculate 3D button in the

Masks tab, or on the button in the Segmentation toolbar, to open the 3D generation

dialog. The following dialog will pop up:


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15.1. Listed masks

Here the created masks (with the lower and higher threshold mentioned) are listed. Select the

masks from which you want to create a 3D.

Note: You cannot calculate a 3D for an empty mask

15.2. Quality

When you calculate a 3D object you can choose the quality. Take low or medium quality if

you want a short calculation time, but the dimensions of the 3D will not be accurate because

of the matrix reduction that is applied on the images! You will get the most accurate result

when you select the optimal quality setting. The high quality setting will still do a matrix

reduction in the XY plane but can give in some situations a smoother and better looking 3D.

Only when you select custom quality you can choose the 3D calculation parameters yourself

by selecting the Custom radio button.

The recommended quality (according to your computer) will be highlighted with a *.

15.3. Calculate

Click the Calculate button to start calculating the 3D. The 3D is automatically shown on your

screen after calculation.

15.4. Options

For more information about the 3D generation parameters, click the Options button.

Here you can set the parameters for the Custom setting for generating a 3D model. 3D

visualization is performed by means of triangulation of a segmented 3D area. The number of

triangles determines the quality of the reconstruction: the more triangles, the higher the

quality. The downside is that more triangles require more memory. This should be considered

when calculating a 3D object.

Two methods for reducing the number of triangles are available: Image matrix reduction

and/or triangle reduction.

A smoothing algorithm changes the overall appearance of the triangular mesh.

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15.4.1. Quality

All these quality aspects are grouped in the predefined Low, Medium and High settings. The

Custom setting is user defined. Especially for technical CT applications (and all high

resolution scans), it is recommended to study the 3D generation parameters and to define

practical custom settings.

15.4.2. Interpolation methods

a. Grey value Interpolation

Grey value interpolation is a real 3D interpolation that takes into account the Partial Volume

effect and therefore it is more accurate. With the grey value interpolation method we assume

that the bone densities give an indication on the amount of bone within one pixel. All edges of

the surface are decided based on the grey values. Also the place in between these 2 pixels is

based on the grey values of the 2 pixels.

The advantage of grey value interpolation is that it gives lots of detail and that the dimensions

are correct. The disadvantage is that you get unnecessary details due to the noise within the

images. With a femur head for instance, you will get better results (meaning: a nicely rounded

edge) when using this grey value interpolation. Of course, you will need to do a little

smoothing as well in order to reduce the noise.

However, it is important to realize that grey value interpolation does not always produce good

results. When the slice distance of the scan deviates considerably from the slice thickness,

the resulting mesh gives a noisy surface. Only if the slice thickness and slice distance are the

same, grey value interpolation works fine. This condition should be fulfilled during the

scanning (acquisition). Changes of the Z resolution (see the paragraph about Matrix

Reduction) therefore should not be used in combination with grey value interpolation. A

reduction of the XY resolution does not violate the condition.


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Grey value interpolation is recommended to use for technical CT applications.

b. Contour Interpolation

Contour interpolation is a 2D interpolation in the plane of the images that is smoothly

expanded in the third dimension. This interpolation algorithm uses the grey value interpolation

within the slices, but in the Z direction a linear interpolation between the contours is used (as

schematically represented below). This interpolation method gives the best results for medical

purposes.

Example of contour interpolation Principle of contour interpolation

Conclusion:

A contour interpolation results in a 3D that looks smoother and better (less gaps). Contour

interpolation is recommended to use for medical CT applications.

A Grey value interpolation results always in correct dimensions and correct positioning of the

3D, but the 3D can be noisy. Grey value interpolation is recommended to use for technical CT

applications.

15.4.3. Shell Reduction

This feature is an extra filter which removes small inclusions by only keeping a number -

defined by the user - of the largest shells.

15.4.4. Slices

By default, the table positions of the first and the last image are shown in the dialog. A default

calculation is a calculation of the whole segmentation.

The calculation can be reduced to a part of the segmentation by adapting the table positions.

The Reset button will restore the default values.

15.4.5. Smoothing

This function is meant to make rough surfaces smoother. It works like a filter for noise

reduction.

The Iteration parameter expresses how many cycles of the smoothing are performed.

Don‟t exaggerate the number of cycles! All iterations change the triangulation. If too many

cycles are passed, every 3D object will turn into a sphere-like object! The number of

iterations defines the area of influence for smoothing.

The Smooth factor indicates the importance of local geometry. If this factor is low (close

to 0), the local geometry is considered as important and the smoothing is limited. With

high values for the ratio (close to 1), the new position is mainly determined by the position

of the other points of the triangles in the neighborhood. In this last case it is obvious that

we talk about smoothing.

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STL generation without smoothing STL generation with smoothing

Note: If you take a high smooth factor, the number of iterations should be kept low.

15.4.6. Matrix reduction

This option allows grouping of voxels to calculate the triangles. The reduction is given relative

to the X-size (= Y-size) of a pixel in the image and relative to the height (Z-size) of a pixel in

the 3D data set.

XY resolution Decides how many voxels are grouped in the XY plane

Z resolution Decides how many voxels are grouped in the Z-direction

An XY- or Z-resolution of 1 means no matrix reduction in the plan or the Z-direction.

Note: When using grey value interpolation, reducing too much will lead to a loss of information for thin or small objects. Artificial holes might appear in the 3D image but the dimensions of the object will stay quite accurate.

Note: When using contour interpolation, reducing too much will lead to incorrect dimensions of the object. The visual representation will be quite good, but when measuring items they will typically appear too large.

If a matrix reduction is set in the plane, you have to option to choose the matrix reduction

algorithm, Continuity or Accuracy.

a. Continuity algorithm

Using this algorithm for matrix reduction in the XY-plane, will give a very nice result, but the

3D dimensions will become larger when using a bigger matrix reduction.

b. Accuracy algorithm

Using this algorithm for matrix reduction in the XY-plane, results in a 3D that is less nice,

because there will appear gaps in the surface on places where the wall thickness is smaller

than the pixel size after matrix reduction. The positive effect is that the dimensions of the 3D

model stay exact.

For the predefined settings (low, medium and high), Mimics automatically selects accuracy for

greyvalue interpolation and continuity for contour interpolation.

15.4.7. Triangle Reduction

Triangle reduction allows you to reduce the number of triangles in the mesh. This makes it

easier to manipulate the file.


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There are three Reducing modes of triangle reduction, the Point-type, the Edge-type and the

Advanced Edge-type. They all have the same parameters. The advanced edge reduction

algorithm generates less noise on the resulting surface and creates a smaller object. The

point reduction and the edge reduction are better for technical objects since they create more

uniform meshes.

The Tolerance indicates the maximum deviation in mm that a related triangle may have, to

be part of the same plane that contains the selected triangle. It makes sense to keep this

value related to the pixel size (e.g. half the pixelsize or a quarter).

The Number of Iterations is a user-set value that defines how many times the program

should make the calculations. The algorithm needs several iterations to reduce the number of

triangles in larger flat areas. This algorithm converges to a stable result after about 15

iterations. More iterations therefore do not make a lot of sense.

The Edge Angle-value defines which angle should be used to determine edges of the part

that cannot be removed. Triangles deviating less than this angle will be grouped into the

plane of the other triangles.

The Working Buffer size relates directly to the amount of memory used to process the

reduction. The higher the buffer size, the greater the part of the segmentation that can be

calculated at once.

It is advisable not to use the reducer on very noisy objects. In this case it is better to perform

a smoothing first.

If a plane, defined by the Tolerance and the Angle consists out of several triangles, the

program will try to re-triangulate this area. The Point-type reduction mode will try to reduce

the amount of triangles by removing a point. The Edge-type will remove a triangles edge (two

points + the connecting line between these two points). If the tolerance-value is too big,

essential part information may get lost.

16. Label

Label Enter label text here

Mask The mask that will contain this label

Font Type of text font. To choose a font, use the Set Font button on the right of the

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Font field.

Size Text size in mm

Depth Depth of the text in mm. The label will start from the current position and will

move upwards, unless the top image is reached, then the label will be copied

downwards.

2D slice-able label Determines if the label is 2D slice-able or not. 2D slice-able labels are

restricted to horizontal or vertical direction.

Horizontal or Vertical Orientation of label

View from top or View

from Bottom Orientation of label

Note: Changing the font of labels is not possible with 2D slice-able labels.

Labels can be exported in STL format in any direction (don't check the 2d slice-able label

button). If you want your labels to be visible in exported sliced files, check the 2D slice-able

label button. When this option is enabled, the labels are restricted to horizontal and vertical

direction.

You can move the label on the images (the mouse cursor changes to a cross). Keep the left

mouse button down and place the label in the desired position (this can be done in all views).

To further edit or delete the created label, click the right mouse button on the label. A pane

appears with the function Delete, which will delete this label, and the function Properties,

which will display the Label Properties Dialog box.

The labels might look incorrect in the 3D View of Mimics. The "View from Top/Bottom" is

related to the Top/Bottom of the stack of images.

17. Cavity Fill from Polylines The cavity Fill from Polylines will create a mask by filling every polyline in a polyline set.

Source polyline set and target mask are set here.

Note: Please be aware that because the cavity fill from polylines, fills polylines that are calculated from a mask and interpolated during this calculation, your new mask can be a bit larger as the original mask.

18. Calculate polylines from 3D The calculate polylines from 3D will create a polylines set from a 3D object or an STL. The

polylines are created by taking the contour of the 3D object or STL on each slice of the project.


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19. Calculate mask from 3D The calculate mask from 3D will create a mask from a 3D object or an STL. The mask is

created by taking the contours of the 3D object or STL on each slice of the project and then

by filling the contour with a mask.

The source 3D object or STL and the target mask can be indicated in the dialog.


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CHAPTER 7: Registration Menu This menu contains the following items:

1. Point Registration The point registration allows you to easily move an STL to a certain location. This is done by

placing one or more sets of landmark points on the STLs, 3D Objects and images. Mimics will

then calculate the transformation matrix that should be applied to have the best fit between

the start and end points and applies that transformation matrix on the selected STLs.

To use this function, first load an STL (File Menu > Load STL). Then go to the Registration

menu and choose the Point Registration function. This will open following interface:

1.1. List of STLs

Name Name of the object.



glasses. You can change the visibility of the contours by clicking on the glasses.

Move Lists if the STL will move when registering another STL. If you e.g. select to register

STL1 on Mask1 and that STL2 should move, STL1 will be registered on Mask1 and

the same transformation matrix will be applied on STL2.

1.2. List of Landmark points

Name Name of the object. By clicking on the name of the object, it can be changed.

Add Point Allows you to add a set of landmark points. You can do this by left clicking on the

images or on a 3D object or STL to indicate the point that has to be moved and then

by doing the same operation to indicate the point where the first point has to move to.

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To register an implant with the point

registration, place landmark points on

both objects.

And apply to find the best fit between the

landmark points and to move the STL to

the new location.

2. Global registration With this operation you can automatically fine tune a previous N point registration. The global

registration will minimize the distance field between two 3D models.

2.1. List of Movable Part





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glasses.

Move Lists if the STL will move when registering another STL. If you e.g. select to

register STL1 on Mask1 and that STL2 should move, STL1 will be registered

on Mask1 and the same transformation matrix will be applied on STL2.

2.2. List of Fixed Part





glasses.

2.3. Settings


Distance threshold

method

If automatic is selected, Mimics will define an automatic distance threshold

based on the geometry.

If manual is selected, the user can specify a distance threshold.

Distance threshold If the distance between a point on the fixed entity and a point on the moving

entity is larger than the threshold value, these points will not be used during

registration.

Number of iterations This number defines how many times the algorithm will be applied

Subsample percentage The subsample ratio defines how many points will be used during

registration. A higher percentage means more points and thus a higher

accuracy but a longer calculation time.

3. STL Registration The STL Registration function allows you to register STLs on masks. To use this function, first

load an STL (File Menu > Load STL) and create a mask of the feature on which the STL

should be registered. Then go to the Registration menu and choose the STL Registration

function. This will open following interface:

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3.1. List of STLs




glasses. You can change the visibility of the contours by clicking on the glasses.

Move Lists if the STL will move when registering another STL. If you e.g. select to

register STL1 on Mask1 and that STL2 should move, STL1 will be registered on

Mask1 and the same transformation matrix will be applied on STL2.

3.2. List of Masks



Lower Threshold Lower Threshold setting of the mask.

Higher Threshold Higher Threshold setting of the mask.

When registering an STL, Mimics will also write out the transformation matrix that was applied

during the registration. The file with the transformation matrix will be saved in the folder of the

Mimics project.

3.3. Settings

You can choose to do a Global Registration or a Local Registration. In general, you want to

do a global registration first and if you would then like to do a feature-based registration, you

can use the local registration.


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3.3.1. Global Registration

The global registration will work on your whole STL. By using the Minimal point distance filter,

you can choose not to use all points of your STL. If you e.g. enter a filter value of 1mm, only

points that have a distance that is higher than 1mm from each other will be taken into account.

Using a filter value will make sure that your result is independent of the density of the STL

and will speed up calculations. If you don‟t want to use the filter, you can just give it a value of

0mm.

3.3.2. Local Registration

The local registration will only work on all points that are within a certain distance of the

border of your mask. By specifying the Maximal distance to mask border filter, you can define

this distance.

The local registration will only work if your STL is already positioned correctly.

3.3.3. Residual Error

The residual error gives you an indication of how good the position of your STL is with relation

to the mask, after doing a registration. The error is a qualitative error, so you can only use this

value for comparing the result when changing the parameters of the registration.

Note: Before doing an STL registration, make sure that your STL is already located in the neighborhood of your mask by using the Translate and Rotate button on the STLs tab in the Project Management.

4. Image Registration The Image Registration function allows you to fuse two datasets by doing a landmark point

based registration. To use this function, you have to first open the base dataset that you want

to use for the registration. Then go to the Registration menu and choose the Image

Registration function. This will open following interface:

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4.1. Load in the second dataset

Next you can load in the dataset that you want to fuse with the base dataset by clicking on the

Browse button. This will open the open project dialog. You can browse through your

hard disk and choose a second dataset from this interface. When you have chosen the

second dataset, Mimics will show this dataset in the views on the right:


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You can use the keyboard and mouse shortcuts for panning, zooming, adjusting the contrast,

scrolling through the images. You can also use the toolbar at the top for panning, zooming.

4.2. Landmark Points

You can add landmark points by clicking on the Add button, then left-click in one of the views

of Dataset 1 and then left-click in one of the views of Dataset 2.

You can delete and locate landmark points by selecting the point from the list and clicking on

the appropriate button.

The landmark points can be moved by left-clicking on one of the landmark points in the views

and dragging the points.

You need at least 3 landmark points to be able to do the registration. You can however

choose to use more points.

4.3. Fusion Method

You can select different Fusion Methods from the list:

Add GVr = GV1 + GV2

If GVr is higher than 4095GV, it is set to 4095.

Subtract GVr = GV1 - GV2

If GVr is lower than 0GV, it is set to 0.

Multiply GVr = GV1 x GV2

If GVr is higher than 4095GV, it is set to 4095.

Divide GVr = GV1 / GV2

GV1 is divided by GV2.

Difference GVr = Abs(GV1 - GV2)

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The absolute value is taken of the difference between GV1 and GV2.

Average GVr = (GV1 + GV2) / 2

The average is taken of GV1 and GV2.

Min GVr = Minimum(GV1,GV2)

The minimum is taken of GV1 and GV2.

Max GVr = Maximum(GV1,GV2)

The maximum is taken of GV1 and GV2.

AND GVr = GV1 AND GV2

A bit wise AND is done of GV1 and GV2.

OR GVr = GV1 OR GV2

A bit wise OR is done of GV1 and GV2.

XOR GVr = GV1 XOR GV2

A bit wise XOR is done of GV1 and GV2.

Transparent GVr = GV1 x (GV2 / 4095)

The grayvalue of Dataset 2 is determining the transparency of the voxels of

Dataset 1.

Opaque GVr = GV2

The grayvalues of Dataset 2 are used. The result is that Dataset 2 is

transformed to the coordinate system of Dataset 1.

4.4. Applying the registration

When you have placed at least 3 landmark points and you have chosen your fusion method,

you can apply the registration. Mimics will then create a new Mimics project that is as big as

Dataset 1.

Dataset 2 will be resliced and registered and the part intersecting with Dataset 1 will be fused

with Dataset 1.


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CHAPTER 8: Export Menu This menu contains the following items:

1. Dicom This function allows converting the imported images into Dicom format. You can also add the

information of the segmentation masks or the contours of 3D objects, providing you with a

straightforward link to virtual surgery navigation systems. You just need to indicate the objects

you want to superimpose on the images and browse to a directory where you want the Dicom

files to be saved. Possible objects are masks, the contours of 3D and CAD objects and STL

files and Simulation objects. You can also specify the thickness of the contour in the DICOM

images.

2. 3dd Allows exporting a mask to a 3dd file.

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You can choose a mask from the list. Then you can choose an output directory by clicking on

the Browse button. You then have to fill in a file name in the File name input box.

3. BMP/JPEG Allows exporting to an image file.

The export of the 2D image(s) is an image that contains the correct pixel size and can thus be

printed in a 1:1 ratio. You can choose to export the Axial, Coronal, Sagittal image and if

available, the Parallel or Cross-section image. You can also export a range of slices.

You need to fill in the root name of the filename, e.g. "Axial", in the filename input box. You

can also choose the type of image file you want to save, bmp or jpg. The image filename will

be constructed with the root name and the slice number, e.g. "Axial-523.bmp", "Axial-

521.bmp", ... You can easily choose the path where the image files will be saved with the

Browse button.


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4. 2D Mask Area Allows exporting a text file with the area of the mask for the specified images of a certain view.

Description of the main areas

Mask This area displays the masks that are currently available in your project.

Select here the desired mask to process.

Images You can choose for which view you want to export the mask area.

Range You can calculate the area of the mask for all the slices in the chosen view,

for the slice that is displayed in the screen or for a specified range of images.

Filename The name of the generated text file

Path When you click the button a window appears. It will act like the

Windows Explorer. You can look at all the drives of your computer and their

directory structure. Select the location where you want your Grayvalues file

to be placed.

5. Grayvalues Allows exporting a text file with the grayvalues of your images.

By selecting Grayvalues in the Export menu, a dialog is displayed where you can choose to

export masks as a text file with all the grayvalues of the voxels.

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Select a mask to

export in Grayvalues

This area displays the masks that are currently available in your project.

Select here the desired mask to process.

Output directory When you click the button a window appears. It will act like the


directory structure. Select the location where you want your Grayvalues file

to be placed.

File name You can change the file name of your Grayvalues file.

Save as type At this time the only possible output format is txt (text file).

Expressed in Choose between Hounsfield units and Grayvalues.

6. Txt The export to Txt allows you to export a text file with the coordinates and the measures of

angle and distance measurements.

By clicking the Add button you add your selection to a queue. You can now export your

selection by clicking on the OK button.

Note: When you also have the MedCAD and the Simulation module, two extra tabs are enabled. The MedCAD module allows you to export the coordinates of CAD primitives. The Simulation module allows you to export the coordinates of the landmark points and reference planes placed with the Measure and Analyze tool.


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Start from

measurements

This area displays the measurements that are currently available in the

project.

Start from MedCAD Shows the different CAD primitives available in the project

Start Measure and

Analyze

Shows the Measure and Analyze point and reference planes available in the

project


Windows explorer. You can look at all the drives of your computer and their

directory structure. Select the location where you want the text file to be

placed.

Objects to convert After selecting an object and clicking the Add button, it will be placed here in

a queue. The files will be processed according to the list.

File name The file name of the txt file.

7. Capture Movie The export movie option allows you to export a movie of your Mimics User Interface while you

are working. When you go to the export menu and choose movie, following interface will

appear:

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Function buttons With these buttons, you can start the recording, pause and stop it. When you

click on the stop button or on the close button, the current movie file is

closed.

Options In the options menu you can choose some general options and some options

for the movie itself:

You can choose to minimize the application during recording, to capture the

mouse cursor, play the movie after recording and to use the auto rotate

function. If the auto rotate function is on, your 3D view will be rotated 360

degrees and this will be exported to a movie.

In the movie options section, you can choose the frame rate of the movie and

the codec that is used to export the movie.

View to capture You can choose to capture the whole application, or only one of the views.

Output Directory When you click the browse button you select the location where you want

your movie file to be placed.

File Name The filename of the movie that will be exported.


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CHAPTER 9: Options Menu The Options menu contains the following items:

1. Register Licenses Materialise Software is key protected. When you start Mimics for the first time or when your

key has expired, the Key Request Wizard will automatically start up to assist you in

registering.

2. Modules In the modules dialog you can display your current license situation or insert a key file

received by e-mail.

3. Preferences In the preference dialog box you can set your preferences that will be applied every time you

start the software. Possible preference settings are:

General General settings like undo settings, autosave settings,...

Visualization Settings about visualization of the indicators, view,...

3D Settings concerning the 3D: the type of rendering, the 3D reference planes,

performance settings,...

Masks Settings about colors and names of masks

Predefined Thresholds Settings about the Predefined Thresholds of the threshold toolbar

Import Settings about preferences for the import wizard

Annotation Settings about the font and background of the annotations

Printing Settings about the pages and objects to print.

Reslicing Settings about the on-line reslice. On-line reslicing is the calculation of the

cross-sectional images and parallel images based on the axial images.

SCSI Settings concerning the 3D: the type of rendering, the 3D reference planes,

performance settings,...

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3.1. General preferences

Working Directories

Default Working

Directory

This directory will act as a default for all actions concerning importing of

images, loading and saving projects, etc... . When you click the button

a window appears. It will act like the Windows explorer. You can look at all

the drives of your computer and their directory structure. Select the desired

directory.

STL Library Working

Directory

This directory will act as the root directory for the STL Library. When you

click the button a window appears. It will act like the Windows explorer.

You can look at all the drives of your computer and their directory structure.

Select the desired directory.

Pixel Unit

Allows you to choose between a GreyValues scale or a Hounsfield scale.


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HIPAA

Hide Filename Select this option to hide all file names, in the open project window, the

project information window, ...

Hide Patient Name Select this option (in combination with the "Hide file name" option) to work in

compliance with HIPAA. The patient name will be replaced by a unique

patient ID in the project information window, the open project window, the

print preview, the printed documentation, ... When saving the study, the

proposed file name will be the patient ID instead of the patient name.

The patient ID contains the initials of the patient and a unique number.

Because the initials are still in the patient ID you can easily differentiate

between the different patients, without having to keep a list with patient ID

and associated patient name. The patient ID cannot be changed.

Note: this function only hides the patient name. When you export the images

to Dicom files and open the images with a Dicom Viewer, you will still see the

patient name. Or, when you exchange the file with another Mimics user, the

other user can turn off the “Hide patient name” option to see the patient

name.

Performance

Always ask to reduce

images when loading

Select this option to have the Reduce Images dialog always displayed when

importing images or when opening a project. More information about the

reduction of images can be found in the section Menu part > File menu

>Open project > Reduce images page.

Maximum Undo Disk

Space

Indicates the maximum disk space that will be used to store information for

the undo and redo operations.

Autosave Settings Select a time frequency from the drop-down list. This gives the frequency

that the project will automatically be saved. Included is also an auto recovery

function when an unexpected event like PC failure would occur. When

opening the software again, it will recover your project you were working on.

Image

When selected Mimics will use less memory for the visualization of the

images.

3-matic

Preset You can select the 3-matic version you want to associate to Mimics. The

“Use Recommended” button selects the highest 3-matic version installed in

your computer.

Path Allows you to browse to the location of the 3-matic version that you want to

use.

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3.2. Visualization preferences

Default Indicators

You can decide if you want to see the tick marks, the intersection lines, the

slice position and/or the orientation strings on your screen. You can also

choose if you want to see all cross-sections or only the active cross-section

and if you want to see full lines or dashed lines.

You can determine the 3D locator to be a Dataset position locator or an

Intersection position locator. The Dataset position locator will indicate the

intersection of the views and the full range of the dataset, whereas the

Intersection position locator will only indicate the intersection. The size of

intersection position locator is expressed as a percentage of diagonal size of

the dataset.

View

You can choose between 3 or 4 panes. In the first case the 3D will replace

the sagittal image in the image layout and the axial image in the reslice

layout. In the 4 panes view, you will see all image views and a 3D view. In


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that case, the Toggle 3D button is not present.

User Interface

To restore the interface items to their default settings click the appropriate

restore button.

Reference Planes

You can choose which views you want to have represented in your reference

planes.

Coordinate System

You can choose if you want to visualize the STL coordinate system, the

Image coordinate system or the World coordinate system.

3.3. 3D Settings

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Rendering

Select OpenGL or Direct3D rendering and select Use Hardware if you have a

graphical card with hardware acceleration. With this rendering you get an

optimal graphical visualization, because the software will look for the card

and use the memory on the card for visualization. If you don‟t have a

graphical card with hardware acceleration, select OpenGL or Direct3D (Use

hardware not selected) or Software rendering.

Visualization and navigation

3D background color Defines the background color of the 3D view. To change this color click on

the colored square.

Use Gouraud shading Enhances the 3D visualization. This setting cannot be selected if you chose

Software rendering.

Use world axis rotation This setting chooses the rotation axis of your 3D object. When the setting is

enabled, the rotation will always be done around an axis perpendicular to the

axial images.

Performance

Unload 3D from

memory when invisible

Frees the memory when the 3D is not shown.

Hide all 3D when

opening a project

Use this option for faster loading of projects. All 3D objects will be set

invisible when you open a project when this option is enabled.

Faster 3D interaction Will switch the 3D to a simplified representation when the frame rate drops

below the selected value.

Light

These parameters define the way in which the part is lighted.

Specular Number: 1

Ambient Number: 20

Diffuse Number: 80


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3.4. Masks preferences

Here you can adjust the default colors of the masks.

Default mask names and colors

Color Allows you to change the color of the selected mask.

Name Allows to change the name tag of the selected mask

Edit Mask in 3D ROI size

Hide 3D objects All 3D objects will be put on invisible when you select to edit the mask in 3D.

Region of interest Allows you to set the dimensions of the region of interest. The 3D mask

visualization tool is a demanding feature, reducing the ROI will make the

visualization faster.

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Restore

Restores all mask preferences to its default settings.

3.5. Predefined Thresholds

List of Predefined Thresholds

Name Name of the predefined threshold

Lower Threshold Indicates the Lower Threshold in the pixel unit, selected in General

preferences.

Higher Threshold Indicates the Higher Threshold in pixel unit, selected in General preferences.

Edit Predefined Threshold settings

Edit Allows you to change the name, the Higher and Lower Threshold value of the


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selected predefined threshold.

Add Allows you to add a new predefined threshold

Delete Deletes the selected predefined threshold

Reset Resets the values of the predefined threshold to their original settings.

Move Up Moves the predefined threshold up in the list.

Move Down Moves the predefined threshold down in the list.

3.6. Import

The import option allows you to set your preferences for the import wizard.

Normal

The normal option sets up default options as in import images wizard description.

This option is recommended when different

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Simplified

The simplified option when selected gives less options in the import images wizard.

When this option is chosen, it does not allow viewing project descriptions and selection

of different studies.

3.7. Nerve

Creation of the nerve

Default diameter Diameter defined as default for the creation of the nerve.

Default color Color defined as default for the creation of the nerve.

Opaque Nerves in

Images If checked, the created nerves will be shown as opaque.


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3.8. Annotation

Visualization

Font Allows you to change the font of the annotation. Select Modify… to visualize

the Font selector dialog.

Box Background color Allows you to choose the background color of the annotation box.

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3.9. Printing preferences

Print Pages

Select the pages to print.

Objects to print

Select the objects to print.

Distance between images

Spacing between the cross-sectional images and the parallel images in the

prints. If the cross-sectional spacing in the prints is not the same as in the

images a message will appear about measurements that may not be visible

anymore.


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3.10. Reslicing preferences

Reformatting images

Distance between

cross-sections

Spacing between two cross-sections.

Distance between

parallels

Spacing between two parallel images

Maximum movement

range

The maximum range of movement for the parallel on both sides of the one

that is originally drawn. This originally drawn curve is at position 0. The real

range can be different on both sides: the real range is limited so that the

parallel curve does not self-intersect. If you draw a curve with a sharp bend,

the movement range inside this bend will be very limited, while it will be the

maximum range at the outside of the bend.

X-ray depth The thickness used to calculate the parallel X-ray.

Snap to fixed positions If you don't select this setting you are able to navigate to virtually every

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of cross-sectionals position you want. Take a look at the picture below. When you click on the

position like indicated with the red bullet, the cross-sectional images will be

shown at the exact position (see blue dotted line) and not to the fixed position

nearby (cyan colored cross-sectional, number 5).

.

Cross-sectional grid

Defines the cross-section grid.


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3.11. Advanced SCSI

To enable Mimics to import Data from a SCSI MOD or Tape reader select Enable SCSI.

Mimics can auto determine which SCSI devices to access therefore select auto determine

and click on start. Mimics will try to detect all the services running on your system. The

software will then check which of these are linked to a SCSI device by sending them a

command. When a service is linked to a SCSI device, it will respond with a certain message.

If it is not linked to a SCSI device, it will ignore this command.

A problem found is that some of these services just generate a system crash when replying to

this command. The "SymEvent" driver of Symantec for example has this effect. Symantec has

created a patch for this problem but some other services may also be buggy.

This List box displays a list of all the services present on your Windows system. It gives you

the possibility to enable or disable sending the command to some of the services. All the

services with a check mark next to them will receive the command. When you click on the

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Start Auto Test button the available services will be automatically marked. If you want to test

a particular service, select the service and click on the Test button.

Note: when Mimics is installed, all SCSI communication is disabled by default. If you want to import from a SCSI device (e.g. a MOD or Tape drive), you have to enable SCSI in the advanced SCSI dialog.


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CHAPTER 10: Help Menu The Help menu contains the following items:


1. General Help Select Help | General Help from the menu to start the help pages at the home location.

2. Context Help Click on the Context Help button or select Help > Context Help from the menu. The cursor

will change to this: .

Click on a button or a menu item to open the help page about that specific subject.

Example:

3. Tutorial The tutorial will start the help pages at the tutorial location.

4. User Community This option will open the website of the Mimics User Community.

5. About The About dialog box displays some information about the system you're working on. If you

encounter any problem with the software, please forward it to Materialise together with your

system information.

Opens the help page about the Toggle 3D button.

Opens the help page about licenses.

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PART IV

Mimics Modules


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CHAPTER 1: Import The import modules allow you to convert images from a variety of scanners to the Mimics file

format. The images can be read from hard disk, floppy, CD, optical disk or tape. When the

data is stored on an optical disk or tape you also need an optical drive that can read the

optical disk or tape.

Importing images from hard disk, CD, MOD and tape is very easy using the Import images

wizard. Importing Dicom, Tiff, Jpeg and Bitmap images from hard disk or CD doesn‟t require a

license, but license passwords are required for all other images that you want to import

automatically. More details can be found on the import licenses page.

More details about the scanners and the devices supported by the Import module can be

found in Overview scanner formats.

Links to the sites of the different drivers and some hardware specifications can be found in

Hardware Specifications.

1. Import licenses To convert images you need one or more licenses, depending on:

The type of images you want to import from hard disk or CD

The type of MOD or tape

No license is needed when you:

Import images manually

Import Tiff or Bitmap images

Import Dicom images from hard disk or CD

For example, if you want to import Dicom images from an Elscint optical disk you need an

Elscint import license. If you want to import native Siemens images from CD you need a

Siemens import license.

Each module can be registered separately or combined. If you don‟t know what module you

need, import some images and Mimics will display the required module.

The provided modules are:

Siemens import module for Siemens scanners

GE Advantage import module for General electric scanners

GE DAT import module for General electric scanners, DAT medium

Philips import module for Philips and Hitachi scanners

GE YMS import module for Yokogawa Medical Systems scanners

Dicom import module for DICOM format

Toshiba import module for the IS&C format of Toshiba scanners

Picker import module for Picker format

Elscint import module for Elscint format

2. Reading from Optical Disk

2.1. Reading from optical disk

Connect the optical drive to your computer and start your computer. Start Mimics and open

the Import images wizard by selecting Import images from the File menu. If your computer

recognized the drive, the drive should already be listed in the favorites list.

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You can click immediately on the drive icon or you can browse for the drive in the Windows

Explorer tree. Select in the tree the SCSI Adapter to access to SCSI devices. A list with the

attached SCSI devices will be shown. When the Import module recognizes the disk or tape

format, this will also be listed (see picture).

Select at the right side of the window the images on the optical disk to convert, click Next and

continue the wizard like described in Step 2 of the Import images wizard page.

Remarks:

If an optical disk is DOS formatted you can access the disk via My Computer >

Removable drive.

When you work on Windows NT, you need to have Administrators rights in order to

access the SCSI devices.

When you have Import problems, read the SCSI troubleshooting page or the Frequently

Asked Questions page. When you need help configuring your SCSI device, read the

Hardware configuration for SCSI devices page.

2.2. Hardware configuration for SCSI drives

2.2.1. Hardware configuration for Pioneer DE-7001 series

At the back of your MO-Drive (Pioneer DE-7001 series) you will find a DIP-switch containing

eight small switches as shown in the next figure. Keep all switches in the position as marked

in this figure, except those to change the SCSI address or those to change the drive operating

mode.

SCSI address Operating mode (WORM - MO)

The first three switches are used for selecting the scsi address, the last two for selecting the

operating mode of the drive (WORM mode or MO mode). Never change these switches

without switching the drive to power-off. (It is not needed to switch off the computer, as long

as the computer performs no operations while the drive is still switched off).


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Setting up the SCSI- address.

The switches 1, 2 and 3 have the values 1, 2 and 4 res. when in the Off position (and a value

of 0 when in the On position). So to calculate the SCSI-address you have to add the values of

the switches in the Off position. e.g. the switch positions in the previous figure give an

address of 2. To generate an address of 5, put the switches 1 (value 1) and 3 (value 4) to On,

and put switch 2 (value 2) to Off, the address is then 1 + 4 = 5 !

Selecting the operating mode.

The switches 7 and 8 are used to select the operating mode of the drive.

Always keep switch 7 in the off position! When switch 8 is in On position, the drive is in

WORM mode. When switch 8 is in Off position, the drive is in MO mode.

2.2.2. Hardware configuration for Pioneer DE-7101 series

At the back of your MO-Drive (Pioneer DE-7101 series) you will find a DIP-switch containing

five small switches. If the SCSI card has SCSI II mode, the driver automatically swaps

between MO and WORM mode when necessary. At the left side of the power button, you will

find a SCSI address selector switch. The drive has to be set as follows:

If there‟s no SCSI II mode, keep all switches in the position as marked in this figure, except

those to change the drive-operating mode. At the left side of the power button, you will find a

SCSI address selector switch.

Never change any of these switches without switching the drive to power-off. (It is not needed

to switch off the computer, as long as the computer performs no operations while the drive is

still switched off).


Pressing the + or - switches on the SCSI address selector will increase res. decrease the

SCSI address. At any time, the selected address is displayed within the window between both

buttons.

Selecting the operating mode (no SCSI II mode).

The switches 4 and 5 are used to select the operating mode of the drive.

Always keep switch 5 in the off position. When switch 4 is in On position, the drive is in

WORM mode. When switch 4 is in Off position, the drive is in MO mode.

2.2.3. Hardware configuration for LMSI LD 520 series

At the back of your MO-Drive you will find a DIP-switch containing eight small switches as

shown in the next figure. An x in the figure means that that side of the button is pressed in.

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Keep all switches in the position as marked in this figure, except those to change the SCSI

address or the one to change the drive operating mode.

The first three switches are used for selecting the scsi address, switch 7 for selecting the

operating mode of the drive (WORM mode or MO mode). Never change these switches

without switching the drive to power-off. (It is not needed to switch off the computer, as long

as no operations are performed by the computer while the drive still is switched off).


The switches 1, 2 and 3 have the values 1, 2 and 4 res. when in the Off position (and a value

of 0 when in the On position). So to calculate the SCSI-address you have to add the values of

the switches in the Off position. e.g. the switch positions in the previous figure give an

address of 2. To generate an address of 5, put the switches 1 (value 1) and 3 (value 4) to On,

and put switch 2 (value 2) to Off, the address is then 1 + 4 = 5.

Selecting the operating mode.

The switch 7 is used to select the operating mode of the drive. When switch 7 is in On

position, the drive is in MO mode. When switch 7 is in Off position, the drive is in WORM

mode.

2.2.4. Hardware configuration for Hitachi OU152S-1 series

At the back of your MO-Drive (Hitachi OU152S-1 series) you will find a DIP-switch containing

4 small switches as shown in the next figure. Keep all switches in the position as marked in

this figure, except if you need to change the termination settings. (Check with your drive

manual for these settings. The settings as in the figure below should be correct.) Right below

the DIP switch you will find a scsi address selector as shown in the figure below.

Never change any of these switched without switching the drive to power-off. (It is not needed

to switch off the computer, as long as no operations are performed by the computer while the

drive still is switched off.)

Setting up the SCSI- address

Pressing the + or - switches on the SCSI address selector will increase res. decrease the

SCSI address. At any time, the selected address is displayed within the window between both

buttons.

2.3. SCSI Troubleshooting

2.3.1. You don't see drives in the SCSI Adapter list

It can be a hardware configuration problem


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Make sure that when you boot your system, you see your device(s) in the list that will appear

on your screen. This list typical displays the SCSI addresses that are in use and will also

display the brand name of the attached devices. If you don't see your device here, check:

if you made a correct termination of your devices

if you made a correct daisy chain when working with several devices.

if your cables are still OK

the dip switch settings of your device

You're working on NT

When you work on Windows NT, you need to have Administrators rights in order to access

the SCSI devices.

You have SCSI Wide

You will need to change some settings in the BIOS of your machine. Typically for the HP

kayak, the settings are set to SCSI wide (32 bits), you need to change that (for the SCSI

address that you will use) to SCSI narrow (16 bits):

Example for an Adaptec AHA 2940 SCSI card in an Alpha PC:

When you boot the PC, press <Ctrl><A> for the SCSI Select Utility - (This message is displayed when

booting, look for something similar)

Select from the menu : "Configure/ View Host Adapter Settings"

Select from the menu : "SCSI Device Configuration"

Now you see a list of all the available SCSI addresses, for the ones you will use for the device drivers,

set "Initiate Wide Negotiation" to NO.

Save the new settings.

This will probably solve your problem. When you boot your PC, check if you see the devices

listed together with their SCSI address. If they still don‟t appear in the list, check if you have

the correct drivers for your SCSI card.

2.3.2. You get the message that you have no license to run this converter

In order to access data via SCSI interface, extra passwords are required. Each module can

be registered separately or combined.

2.3.3. Blue Screen on pressing import button

When you have a blue screen from the moment you click on the Import button, check the

Advanced SCSI Options (for Windows NT).

2.3.4. Unknown medium

This might sound stupid, but also try reading the other side of the disk.

3. Reading from tape Dumping data from tapes must not be confused with the automatic conversion of GE HiLight

Advantage tapes. When the files from a tape are dumped, the conversion still needs to be

performed. The conversion is then similar as Importing images from hard disk.

Picker tapes are tapes that can be dumped using the Eliant 820 from Exabyte. Typically all

images are stored in one file that is the fourth one on the tape. Sometimes there is also a fifth

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file containing some images. The third 'file' on a Picker tape is some blank data that needs to

be skipped.

Picker tapes can be read as follows:

Click on SCSI Adapter, this line is shown: "EXABYTE: Picker tape".

Select this line and click on the Dump button . The following parameter window is

displayed:

Since typically all images are stored in the fourth file (or partition), you need to dump this file.

It is this "Dumpfile" (with *.dmp extension) that needs to be converted afterwards. The dump

file is stored in the Target directory you‟ve set in the Tape Dump Parameters window. To

import this dump file, follow the instructions as described in the Import section of Mimics (see

picture below).


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Other tapes than Picker tapes can be dumped as well in a similar way. Then you need to try

out yourself on what partitions the data is stored.

Several messages can appear while dumping the tape. If Mimics is reading an empty partition

you get the following message:

Answer Yes if you want to skip the empty partition and continue reading the next partitions.

Answer No to stop reading.

If there are no other readable partitions on the tape, you get the message:

When the end of the tape is reached, the following message is displayed. It means that 6

dump files have been made.

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4. Dicom Input Application The Dicom Input Application allows you to receive Dicom images that are sent via a Dicom

network. The Dicom images are stored on your computer in a local folder (DIA folder), which

can be chosen during installation. When the Dicom input application is installed and licensed,

you will notice a yellow folder icon on the bottom right corner of your desktop.

When Dicom images are received, a message will be displayed to inform you. The received

images can be viewed via Windows Explorer or via the Import Images Wizard. Start the

wizard by selecting Import Images in the File menu or by clicking on the Import button in

the toolbar.

In the Import Images Wizard, click the DIA button to visualize the images stored in

the DIA folder. Then select the files to import and click on the Next button. When new images

are received, you need to update the DIA database by clicking on the Rebuild DIA Database

button . Continue the import operation following the steps described in the help pages

about the Import Module.

4.1. Installing the DIA

The DICOM Input Application or DIA is a licensed feature that allows you to receive images

via a DICOM network.

We recommend that you close all other applications before installing the DICOM Input

Application. If you are running Windows NT or Windows 2000, you must have administrative

privileges to install the software. During the installation of the DICOM Input Application,

following dialogs will be shown:

STEP 1:


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Wait until the progress bar is finished and then click Next to proceed.

STEP 2:

After reading the license agreement, click the Yes button.

STEP 3:

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The DICOM Input Application will be installed in the directory:

C:\Program Files\Materialise\DICOM Input Application.

If you prefer another directory, select an existing directory by clicking on Browse. Click Next

to proceed.

STEP 4:

Program icons will be added to the Program Folder > Materialise Software. If you want

another folder name, then type a new name or select one from the existing folder list.

STEP 5:


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Enter the workstation‟s AE Title, IP address and port number assigned by your network

administrator. Click Next to proceed.

STEP 6:

The installation program suggests a folder on your computer to store all images that will be

received via a DICOM network. Click Next to proceed if you agree with the chosen folder. If

you want DIA to use another folder, click Browse and choose a new destination folder.

STEP 7:

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When everything is filled in like you want, click Next to proceed. If you want to change or

review something, click Back.

STEP 8:

The DICOM Input Application gets installed. This can take a few moments. This window will

close automatically when the progress bar is finished.

STEP 9:

The software is successfully installed. Click Finish to close the installation dialog. It‟s

recommended to reboot your computer to finalize the installation.

STEP 10:


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When you reboot the system, the DICOM Input Application will start automatically and will ask

you if you want to register it. For more information about the registration process, please look

at the Registration help page.

To uninstall the DICOM Input Application, go to Start > Settings > Control panel >

Add/Remove programs. Select DICOM Input Application and click the Remove button. All

DIA folders will be removed.

5. Overview of supported images

5.1. DICOM

Mimics supports the latest DICOM 3.0 standard but also previous ACR-NEMA formats (1.0

and 2.0). The DICOM format is a standard in the Medical Imaging world and most recent

scanners are DICOM compliant.

Mimics can import DICOM images that are compressed with the JPEG algorithm. Both lossy

and lossless JPEG compression is supported.

Even DICOM images made with cone beam scanners from Morita and NewTom scanners

and proprietary images made with cone beam scanners from Aracor are supported.

5.2. BMP, TIFF, JPEG

Mimics supports BMP, TIFF and JPEG images. The properties of these images are

recognized automatically and you only have to fill in the information about the data set (e.g.

patient name, pixel size and slice increment).

5.3. User-defined Import

If the image format is not supported but you know all the properties of the images (pixel size,

image size, slice distance…), you can also do a manual import of the images.

The only restriction when importing images manually is that the images have to be

uncompressed.

5.4. Proprietary Formats

Beside these image formats that are supported by the Mimics base module, we also offer

different Import Modules. With every Import Module, you can import several proprietary

formats from scanner manufacturers. Different types of media and devices are supported.

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Below you can find a list of some of the scanners, devices and media we support. If your

scanner is not on the list, please contact us. It could be that we already support your scanner

or that we can provide you with a solution for your type of scanner.

5.4.1. Supported Scanners

Asahi Roentgen PSR9000N

Elscint CT twin

Elscint Elite

Elscint Exel 2400

Elscint Omnipro

Elscint Twin

GE 9800

GE Advantage

GE CT/e, Dual

GE GEMS Jupiter, Zeus, ZeusRP

GE Hilight Advantage

GE HiSpeed, QX/i, RP

GE Lightspeed, 16, Plus, QX/i, Ultra

GE Prospeed

GE Sytec

GE CT Pace

GE Sigma (MR)

Hitachi MRP 7000

Hitachi W2000

Hitachi W950

Philips Aura

Philips Brilliance

Philips Easyvision *

Philips Mx 8000, Dual, IDT

Philips Secura

Philips Tomoscan 60/TX, TX, CX, CX/S, CX/Q,

LX, LX/C, SR

Picker MxTwin

Picker PQ, 2000, PQ 5000, PQ 6000

Shimadzu SCT

Siemens Balance

Siemens Emotionm Duo

Siemens Esprit Plus

Siemens Magnetom (MR scanner)*

Siemens Sensation 4, 6, 10, 16

Siemens Somatom 4 AR *, 4 Plus, AR*, AR/SP,

DRH*, HiQ*, Plus*

Siemens Volume Zoom *

Toshiba

Toshiba Aquilon

Toshiba Asteion

Toshiba IS&C Format

Toshiba Xpress

Toshiba Xvision

Yokogawa ProSpeed

* Uncompressed image files are required


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5.4.2. Supported Devices

4 mm tape drive

Exabyte Eliant 820 (8200 format)

Hitachi 5” Optical disk drive type OU152S-1

LMSI LD 520 MOD-WORM devices

Max Optix drive type T4-2600

Max Optix drive type T5-2600

Pioneer DE-7001 series

Pioneer DE-7101 series

Pioneer DE-H9101 series

Sony RMO-S551

5.4.3. Supported Media

5.25 inch MOD like MaxOptix, Verbatim, Sony...

4mm DAT tape

8mm DAT tape

Maxell LM510

Maxell OC-112P-2

Maxell OC-112P-2

MaxOptix

Pioneer DC-17GWO

Pioneer DC-502

Pioneer DEC-17GMO

Pioneer DEC-702

Verbatim

General Remark: Every disk drive has a limited capacity that it can handle, always check on the physical compatibility between the disk and the drive.

More information about the devices can be found on following web-pages:

MaxOptix drives: http://www.maxoptix.com/ Pioneer drives: http://www.pioneer-eur.com/pioneer/deskpage.jsp?taxonomy_id=43 Exabyte, Eliant 820 tape drive: http://www.exabyte.com/products/products/eliant.cfm Sony drives: http://www.sel.sony.com/SEL/rmeg/data/


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CHAPTER 2: RP Slice RP Slice interfaces from Mimics to Rapid Prototyping systems via sliced files to build models.

Optimal accuracy is achieved in a very short time by the direct conversion of the images to

several sliced machine file formats: SLI and SLC for 3D Systems, CLI for Eos). High order

interpolation (bilinear and inter plane) algorithms result in excellent surface reproduction from

scan to model. RP Slice supports color stereolithography: tumors, teeth and teeth roots, nerve

channels can be highlighted in the RP model, giving an extra dimension. Patient information

can be displayed by a punched or colored label.

One of the major difficulties in Stereolithography and most other Layer Manufacturing

techniques is the need for support structures. Both the generation (automatic or manual) and

the removal of these support structures are complex problems: not enough or not strong

enough supports are causing inaccuracies; too much or too strong supports are resulting in

bad surface quality and/or a lot of cleaning work.

The basic function of the support structure is to support the part during the building process.

The whole part is connected with a platform, and 'islands' which are isolated at a certain

moment during the process need to be attached with the rest of the part.

Another function of the supports is to reduce curling effects. Stereolithography resins have a

tendency to deform during the building process because of internal stresses generated by the

shrinkage. By building a strong support structure under a part, this deformation can be

minimized.

When Stereolithography is used starting from a CAD representation, the support structures

can be designed in the CAD system. This is a large work, sometimes exceeding the drawing

work of the part itself. For that reason, software was developed in the past to generate

automatically support structures starting from an STL description of the part, e.g. Magics RP.

In some instances however, one is not able to generate a support starting from an STL

description. This is the case in medical applications where the layer information of the CT

scanner is interfaced directly to the layer information of the Stereolithography machine. This

means that there is no surface information available and the standard techniques for

automatic support generation cannot be used. In addition the manual generation of the

supports is impossible because the information is not present in a CAD system.

The solution developed at Materialise has been called "RP Slice". This module allows you to

calculate contour files and support structures starting from these contour files.

1. Starting RP Slice All RP Slice functions are loaded immediately in Mimics after registration of the RP Slice

module. The RP Slice dialog can be started in one of the following ways:

Via the main toolbar:

Select the RP Slice button

Via the menus:

Select RP Slice from the File menu.

Select a contour format (CLI, SLI or SLC) from the Export menu. This opens the RP Slice

dialog with the chosen contour format already selected.

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Via the Project Management:

You can open the RP Slice dialog by selection the RP slice icon in the Action list of the

Mask tab.

Note: If you're not able to start RP Slice, you probably haven't entered the passwords yet. Go to Options > Licenses and fill in the correct passwords.

2. Exporting contour files

2.1. RP Slice Mask or File selection

In the RP slice dialog you start with the selection of one or more masks, 3dd files or contour

files. When no project is opened in Mimics or when only the STL+ module is licensed (and not

the Mimics basic module) you can only select 3dd or contour files.

By clicking the Add button you add your selection to a queue. Remark that you are not

allowed adding a combination of masks, 3dd files and contour files. All files in this queue will

be exported in the selected output format and will be saved in the selected output directory.

To generate a contour file, start with selecting a mask or 3dd file. To generate a support file,

start with selecting a contour file. Depending on the selection, different dialogs will be shown

after clicking the Next button.


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2.1.1. Description of the main areas

Start from Mask This area displays the masks that are currently available in your project.

Select here the desired mask(s) to process.

Start from 3DD file If you have a .3dd file you wish to process, press this button in order to go to

the RP Slice file selection window.

Start from contour file If you have a contour file for which you want to generate the support

structure, press this button in order to go to the RP Slice file selection

window.


Windows explorer. You can look at all the drives of your computer and their

directory structure. Select the location where you want your support files to

be placed.

Masks/3dd/contour files

to convert

After selecting a mask, 3dd file or contour file and clicking the Add button, it

will be placed here in a queue. The files will be processed according to the

list.

Selecting the files and pressing the Remove button removes the files from the

queue. Clicking on the files in the Output Filename column allows changing

the file name.

Output Format The possible output formats are CLI, SLI and SLC.

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2.2. RP Slice/STL+ to CLI, SLI, SLC, IGES

This function will generate files for different Rapid Prototyping Systems. The files are very

close to machine files and contain all the vectors which will be used on the RP machine. For

the stereolithography machine, both the contours and the internal hatchings will be generated.

Note: It is advised to use these functions for interfacing to the RP machine whenever possible. The functions provide higher order interpolation algorithms and give the most accurate and highest resolution models possible. Only when no direct interface is provided, and in some other restricted cases, it might be better to use the STL interface.

2.2.1. Slice Positions

Position First Slice The table position of the image data set has to be entered. Standard the

lowest position will be displayed.

Position Last Slice This table position indicates up to where the part should be made. Standard

the highest position will be displayed.

If you want to build the entire mask or file, you don't have to change anything here.

If the model is too high to fit in the RP machine, or the user wants to build it in two pieces, one

can process the same file twice: one time from the start to the middle, another time from the

middle to the end. It is also possible to build a part in two pieces with one part from top to

middle and the other from end to middle. In this way the pieces will fit better.

This can be interesting when building a complete skull or if one wants to avoid supports inside

the skull.


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2.2.2. Build Direction

Here you can toggle between ascending or descending:

Ascending: the lowest table position will be built first. The highest table position will be

built last.

Descending: the highest table position will be built first. The lowest table position will be

built first.

The program will take care of mirroring. Sometimes building the model upside down is

preferred because less support is needed in this direction.

2.2.3. Cubic Interpolation

Two inter-slice interpolation schemes are implemented: Cubic and linear interpolation. Linear

is the default as it is faster and gives good results in cases with small slice distances. Cubic

interpolation will give smoother surfaces as show in the next figure.

In the figure, the dashed lines show linear interpolation between 4 points of a contour, the full

lines show the cubic interpolation. If the original images are only 1 mm separated, a linear

interpolation is in most cases good enough. When the slices are 2 or more millimeters

separated it is advised to use the cubic interpolation.

In the image you see a comparison between linear interpolation and cubic interpolation. The

black dots are the original contour points, the small vertical lines mark the interpolation

distances. The solid line is the cubic interpolation and the dashed line shows the linear

interpolation.

2.2.4. Labels

This radio button determines whether the label will be in color (color stereolithography only) or

punched.

Choose the option "none" when there is no label.

2.2.5. Color Stereolithography only

If a part needs to be built in color, the checkbox should be marked.

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Clicking the Next button will link you to the RP Slice calculation parameters page.

2.3. RP Slice Calculation Parameters

2.3.1. Hatching parameters

X hatching space For interfacing to a 3D systems SLA 250 (SLI files), it is possible to create

directly the vector files for the machine. This will speed up the procedure

even more.

This parameter defines the distance between the hatchings on the

Stereolithography machine.

For other output formats this parameter has no influence.

Y hatching distance Same as in X but in the Y direction.

X color hatching space For creation of a model with colored regions, one can define the hatching

space for the coloration. Mostly this value is the half of the X hatching space.

Y color hatching space Same as in X, but in the Y direction.

2.3.2. Build parameters


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Layer thickness This parameter defines the output layer thickness in mm. It must be chosen in

function of the Rapid Prototyping machine and its material.

For having an acceptable surface quality a layer thickness of maximum 0.25

mm is advised. It is a good compromise between model quality and build

time.

For epoxy resins (Stereolithography) with a low penetration depth, a layer

thickness of 0.15 mm is faster than 0.25 mm.

Slice Resolution This value determines the internal representation of the output file: the units

are one over the slice resolution. If the slice resolution is 100, the values in

the output file are 1/100 mm.

The higher the slice resolution, the more accurate one can work. On the other

hand, a higher slice resolution gives a smaller working space. If you

encounter contours which are cut off at a certain maximum x and y value, it is

possible that the slice resolution is too high.

Some examples :

Slice Resolution Units Maximum

dimensions

200 0.005 mm 327 mm

100 0.01 mm 535 mm

80 0.0125 mm 819 mm

Note: on the 3D systems SLA only resolution 40, 80 and 200 are supported.

First layer height The first layer height gives the value of the translation according to the

direction of building in mm. In this way support height can be chosen

afterwards by choosing the start of the support (e.g. support starts at 0 mm,

the part at 10 mm, or support starts at 6 mm, the part at 10 mm).

Scale factor This parameter allows you to rescale the original object with a factor larger

than 0.1 and smaller than 100.

2.3.3. Filters

These parameters filter out data points of the contours in order to reduce the file size and thus

the calculation time.

Minimal Segment Length When the distance between two points is smaller than the minimal segment

length, one of the points will be removed.

This:

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becomes

Out of Line Distance When the distance between a point and a line – constructed by two other

points – is smaller than the out of line distance, this point will be removed.

This

becomes

Minimal Contour length These parameters will remove contours whose length is longer than the

parameters set.

2.3.4. Restoring Defaults


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Pressing the Restore Defaults button restores the parameter values to their original values.

These are stored in a file called material.ini which you can find in the installation directory.

Pressing the Finish button starts the RP Slice calculation which runs in a separate program

so you can continue to work in Mimics.

3. Support Generation After the creation of a sliced file, you can also generate a support file. To do this, go again to

RP Slice and choose to generate a file from a Contour file:

Select the type of the Input and Output file, add the desired file and click on Next. You will

then go to step two of the RP Slice wizard where you can choose different parameters for

your support file.

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3.1.1. Hatching Parameters

X Hatching Space The distance between two support walls in the x-direction.

Y Hatching Space The same in the y-direction.

3.1.2. Perforation

Perforation Length Distance (1) in the drawing below. (must be smaller than half the hatching

distance)

If this value is 0, the perforation option is off

Perforation Angle Angle (2) in the drawing below.

Nr. of straight layers The length of the straight part: distance (3) expressed in numbers of layers.

Perforated Borders When this is checked, the perforation will also continue on the borders of the

support.


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3.1.3. Support

Angle The maximum angle which can be built without support. All surfaces which

are flatter than that angle will become supported (angle in function of the

horizontal plane, in degrees).

Starting Height Starting height of the support structure (see picture). Be aware that the

support will not go below 0 (in the z-direction).

Ending Height All features higher than the Ending Height will not be supported (see picture).

This is useful if you know that no supports are needed higher than a certain

height. For instance, if you build a complete skull, in a lot of cases, no support

is needed inside the skull. By putting this parameter above the orbits, no

supports will be created for the cranium.

You can calculate the Support Ending Height by calculating the height of

support via table positions in Mimics and adding the First Layer height

(parameter from STL+).

Instead of specifying an ending height one can also select the Full Height

option. This will force the support to be build up to the top of the part, where

needed (see picture).

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XY Offset If you don't want the support to damage vertical walls, it might be interesting

to use an xy-offset for the support generation. This value will determine how

far the support must be separated from the part.

Depending on which file format you have chosen, some of these parameters will be of no

interest. In that case they will be disabled so that the box to fill in the parameters is not

accessible.

3.1.4. Restoring Defaults

Pressing the Restore Defaults button, restores the parameter values to their original values.

These are stored in a file called material.ini which you can find in the installation directory.

Pressing the Finish button starts the RP Slice calculation which runs in a separate program

so you can continue your work in Mimics.

4. How to work with sli files on the 3D systems SLA

250? The sli files are the most direct way to make models on the SLA 250. STL however it is an

internal 3D systems file format which is not directly supported by Partman. But, there is an

easy workaround to bring these files on your machine.

Generate the sli file with RP Slice (e.g. name.sli). Make sure that the x and y hatching spacing

are filled in correctly. Together with the sli file, the program will also generate a dummy stl file

with the same name as the sli file, but with extension stl (name.stl): this stl file is just a box

with the same dimensions as the slice (sli) file.

Generate support for the sli file with the RP Slice program (generate also an sli file):

s_name.sli

On the Unix prompt type: cp name.stl s_name.stl (depending upon your file name)

In Partman you can translate the file s_name.stl downwards in the z-direction with the same

amount as the height of the support (save it again). In this way we have a stl file with the

same position as our support sli slice file.

Do the normal preparation in Partman with the "s_name.stl" and "name.stl" as you do for

normal stl files (including support settings, ranges etc.…)? When you are finished, save the

spreadsheet. (File / Save) and clear (File / Clear)

In Partman do: File / UNIX. And type: "touch *.sli" [enter] exit [enter].

In Partman do: File / Load (your spreadsheet file)

Then prepare your parts with "Prepare" (choose "prepare" and not "prepare all") The program

should tell you that the files are already sliced, and it will directly generate the machine files.

Copy the machine files to your SLA computer, and build your parts.


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5. RP Slice and Lightyear This section will give an explanation about how to make models in Mimics that can be built on

3D Systems SLA machines. We will use Mimics, RP Slice and Lightyear to make the link

between Mimics and the SLA machine.

Most of the time exporting the models to STL and then importing them in Lightyear is very

difficult because of the size of the files. It is far better to use the RP Slice module to make a

sliced file of the model.

The main advantages of this approach are:

No Problems with big files, because it is already sliced

Cubical interpolation can be applied. The model will look less stair-stepped.

High resolution can be maintained.

Support Generation: the perforated supports save material, are easier to clean and can

be build faster (up to 4 times as fast)

Note: This procedure was tested on Lightyear 1.3.

5.1. Create a sliced file

The first step in the process is making a sliced file from your model. RP Slice can export to

three different sliced formats:

CLI: Common Layer Interface

SLI: 3D Systems Layer Interface file

SLC: 3D Systems Layer Contour file

The latest version of Lightyear is only compatible with the SLC format, so we will use this

format.

To export the model to an SLC file, click on File -> RP Slice or click on the RP Slice button on

the main toolbar: .

This will bring up following interface:

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You can export sliced files from Masks, 3dd-files or Contour Files. To export from a mask,

select a mask and click on the Add-button. This will list the mask in the list of the files that will

be converted. Now select the SLC format as the Output format. You can also change the

name of the sliced file by clicking on the output file name.

When you click on the Next button, you can adjust the slice positions, the build direction and

choose if you want to use cubic interpolation:


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When you click again on the Next button, several other calculation parameters can be

adjusted. For more information about these parameters, please refer to the calculation

parameters page.

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Note: To make the import process in Lightyear faster, please make sure the Layer Thickness of the sliced file is the same as the layer thickness that you will use in Lightyear.

When you then click on the Finish-button, the conversion process is started and the sliced file

is saved.

Saving sliced files from a 3dd file is done in the same way. Just select the 3dd tab on the first

screen.

5.2. Generate the support file

To generate a support file for a sliced file, click on File -> RP Slice or click on the RP Slice

button on the main toolbar: .

This will bring up following interface:


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Select the tab Contour Files. Now select the SLC format as the Input and the Output format

and then browse to the directory where you have saved your sliced file. You can then add the

file with the Add button.

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When you click on the Next button, you can adjust several support generation parameters.

For more information about these parameters, please refer to the support generation page.


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When you then click on the Finish button, the support generation process is started and the

support file is generated.

5.3. Open the files in Lightyear

In Lightyear, go to File and then Open File. You can then browse to the directory where you

have saved the sliced file and the support file. Select both files and click on Open. Both the

model and the supports will then be loaded in Lightyear and can then be prepared for building

on the SLA machine.


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CHAPTER 3: STL+ The STL+ module provides interface options via triangulated formats: Binary STL, ASCII STL,

DXF, VRML 2.0 and PLY.

Using the STL+ module, a triangle mesh will be generated around the selected volume. The

number of triangles determines the quality of the reconstruction: the more triangles, the higher

the quality. The disadvantage is that more triangles require more memory. The STL+ module

provides powerful tools to perform a significant reduction of the file size. Read more about this

on the STL+ calculation parameters page.

1. Exporting triangulated files All STL+ functions are loaded immediately in Mimics after registration of the STL+ module.

The STL+ dialog can be started in one of the following ways:

Via the main toolbar:

Select the STL+ button

Via the menus:

Select STL+ from the File menu

Select an STL+ output format (Binary STL, ASCII STL, DXF, VRML or PLY) in the Export

menu. This opens the STL+ dialog with the chosen output format already selected.

Via Project Management:

Select the action button in the mask or 3D tab and select the STL+ icon.

Note: If you're not able to start STL+, you probably haven't entered the passwords yet. Go to Options > Licenses and fill in the correct password.

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1.1. STL+ mask, 3D or file selection

In the STL+ dialog you start with the selection of one or more masks, 3D objects, 3dd files,

CAD objects or FEA meshes. When no project is opened in Mimics or when only the STL+

module is licensed (and not the Mimics basic module) you can only select a 3dd file.

By clicking the Add button you add your selection to a queue. Remark that you are not

allowed adding a combination of masks, 3D objects, 3dd files, CAD objects and FEA meshes.

All files in this queue will be exported in the selected output format and will be saved in the

selected output directory.

When masks or 3dd files are added to the queue, the 3D calculation parameters dialog will

appear after clicking the Next button. After completing these parameter values the files will be

exported.

When 3D objects, CAD objects or FEA meshes are added to the queue, all objects will be

exported immediately after clicking the Finish button.


Start from Mask This area displays the masks which are currently available in your project.

Select here the desired mask(s) to process.

Start from 3D This area displays the 3D objects that are currently available in your project.

Select here the desired 3D object(s) to process.

Start from 3dd File If you have a .3dd file you wish to process, press this button in order to go to

the STL+ file selection window.

Start from CAD This area displays the CAD objects that are currently available in your project.

Select here the desired CAD object(s) to process.

Start from FEA This area displays the FEA meshes that are currently available in your

project. Select here the desired FEA mesh(es) to process.




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directory structure. Select the location where you want your triangulated files

to be placed.

Output Format The possible output formats are Binary STL, ASCII STL, DXF, VRML 2.0,

PLY and single PLY file. VRML files can be used as input to Virtual Reality.

When exporting multiple objects to a single PLY file, Mimics will create one

PLY file that contains all objects. The color of the objects will also be saved,

enabling you to create multi-color objects suitable for color 3D printing.

Objects to convert After selecting a mask, 3D object or 3dd file and clicking the Add button it will

be placed here in a queue. The files will be processed according to the list.

Selecting the files and pressing the Remove button removes the files from the

queue. Clicking on the files in the Output Filename column allows changing

the file name.

Scale factor You can scale your object by changing the value in the edit field.

1.2. STL+ - STL / VRML Parameters

The STL/VRML interface will generate a triangle mesh around the selected volume.

The number of triangles determines the quality of the reconstruction: the more triangles, the

higher the quality. The downside is that more triangles require more memory. This should be

considered when calculating an STL file.

Two methods for reducing the number of triangles are available: Image matrix reduction

and/or triangle reduction. The Triangle reduction algorithm reduces the file size (the amount

of triangles) keeping the STL surface as close as possible to the original one (e.g. without

decreasing the resolution). It will search for (approximately) flat surfaces in the STL file and

reduce the amount of triangles to fill in these surfaces.

The method used to interpolate the images and generate the 3D triangular mesh can be

chosen out of two options: grey value interpolation and contour interpolation. For medical

applications the contour interpolation gives nicer results, for technical applications grey value

interpolation is preferred

A smoothing algorithm changes the overall appearance of the triangular mesh.

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1.2.1. Quality

All these quality aspects are grouped in the predefined Low, Medium, High and Maximum

settings. The Custom setting is user defined. Especially for technical CT applications (and all

high resolution scan‟s), it is recommended to study the 3D generation parameters and to

define practical custom settings.

1.2.2. Method

Basically, Contour interpolation is a 2D interpolation in the plane of the images that is

smoothly expanded in the third dimension. Grey value interpolation is a real 3D interpolation

and therefore more accurate. However, it is important to realize that grey value interpolation

does not always produce good results. Only if slice thickness and slice distance are the same,

grey value interpolation works fine. First of all, this condition should be fulfilled during the

scanning (acquisition). Secondly, changing the Z resolution (see below) will most likely result

in a violation of this condition because the slice distance for the calculation will increase.

Changes of the Z resolution therefore should not be used in combination with grey value

interpolation. A reduction of the XY resolution does not violate the condition.

Contour interpolation is recommended to use for medical CT applications.

Grey value interpolation is recommended to use for technical CT applications.

1.2.3. Slices

Default, the table positions of the first and the last image are shown in the table. A default

calculation is a calculation of the whole segmentation.

The calculation can be reduced to a part of the segmentation by adapting the table positions.

The Reset button will restore the default values.


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1.2.4. Scaling

The scaling option allows you to scale the part during export. This way you can e.g. easily

build demo parts on a scale of 50% (value 0.5).

1.2.5. Matrix reduction

This option allows the grouping of voxels to calculate the triangles.

The reduction is given relative to the X-size (=Y-size) of a pixel in the image and relative to

the height (Z-size) of a pixel in the 3D data set.



Note: When using grey value interpolation, reducing too much will lead to a loss of information for thin or small objects. Artificial holes might appear in the 3D image but the dimensions of the object will stay quite accurate.

When using contour interpolation, reducing too much will lead to incorrect dimensions of the

object. The visual representation will be quite good, but when measuring items they will

typically appear too large.

1.2.6. Smoothing

This function is meant to make rough surfaces smoother. It works like a filter for noise

reduction.

The Iterations parameter expresses how many cycles of the smoothing are performed. Don‟t

exaggerate the number of cycles! Every iteration changes the triangulation. If too many cycles

are passed, every 3D object will turn into a sphere-like object! The number of iterations

defines the area of influence for smoothing.

The Smooth factor indicates the importance of local geometry. If this factor is low (close to 0),

the local geometry is considered as important and the smoothing is limited. With high values

for the ratio (close to 1), the new position is mainly determined by the position of the other

points of the triangles in the neighborhood. In this last case it is obvious that we talk about

smoothing.

You can also choose to use a shrinkage compensation. The Compensate shrinkage option

will make sure that the volume of the part before smoothing and after smoothing is similar.

Using the shrinkage compensation will have a negative effect on the speed of the calculation.

Note: if you take a high smooth factor, the number of iterations should be kept low.

1.2.7. Triangle Reduction

Triangle reduction allows you to reduce the number of triangles in the mesh. This makes it

easier to manipulate the file.

There are three Reducing modes of triangle reduction, the Point-type, the Edge-type and the

Advanced Edge-type. They all have the same parameters. The advanced edge reduction

algorithm generates less noise on the resulting surface and creates a smaller object. The

point reduction and the edge reduction are better for technical objects since they create more

uniform meshes.

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The Tolerance indicates the maximum deviation in mm that a related triangle may have, to be

part of the same plane that contains the selected triangle. It makes sense to keep this value

related to the pixel size (e.g. half the pixel size or a quarter).

The Number of Iterations is a user-set value that defines how many times the program should

make the calculations. The algorithm needs several iterations to reduce the number of

triangles in larger flat areas. This algorithm converges to a stable result after about 15

iterations. More iterations therefore do not make a lot of sense.

The Edge Angle-value defines which angle should be used to determine edges of the part

that cannot be removed. Triangles deviating less than this angle will be grouped into the

plane of the other triangles.

The Working buffer size relates directly to the amount of memory used to process the

reduction. The higher the buffer size, the greater the part of the segmentation that can be

calculated at once.

It is advisable not to use the reducer on very noisy objects. In this case it is better to perform

a smoothing first.

If a plane, defined by the Tolerance and the Angle consists out of several triangles, the

program will try to re-triangulate this area. The Point-type reduction mode will try to reduce

the amount of triangles by removing a point. The Edge-type will remove a triangles edge (two

points + the connecting line between these two points). If the tolerance-value is too big,

essential part information may get lost.

2. Modifying triangulated files The STL+ module does not only allow you to export triangulated files, but also to modify the

STL files for result optimization.

The 3D Tools can be started in one of the following ways:

Via the Tools toolbar:

Select the button corresponding to the function you want to perform

Via the Tools Menu

Select the function from the Tools Menu. This will open the corresponding dialog window.

2.1. Smoothing

The smoothing tool allows you to smooth 3D Objects or STLs. The result of the smoothing

operation will be put in the 3D Objects list.

To launch the smoothing tool, select the corresponding option from the Tools menu.

The following window will pop up:


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Functions on Objects to Smooth

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to

change the visibility of the object.

Contour visible Lists if the contour of the object is visible or not by means of glasses. Click on

the glasses to change the visibility of the contour of the object.

Show only

selected objects

Makes the selected objects visible and the unselected objects invisible.

Iterations You can choose how many smoothing iterations will be performed.

Smooth factor The smooth factor determines how much smoothing is performed.

Compensate shrinkage If the compensate shrinkage setting is enabled, the shrinkage of the object

due to the smoothing will be countered.

Keep originals If the keep originals checkbox is checked, the original objects will be kept,

otherwise they will be deleted and only the cut objects will remain.

2.2. Triangle Reduction

The triangle reduction tool allows you to do a triangle reduction of 3D Objects or STLs. The

result of the triangle reduction operation will be put in the 3D Objects list.

To launch the triangle reduction tool, select the corresponding option from the Tools menu.


Functions on Objects to Reduce Triangles





Show only selected

objects


Reducing mode You can choose between a Point based triangle reduction, an Edge based

triangle reduction or an Advanced Edge based triangle reduction.

Tolerance The Tolerance indicates the maximum deviation in mm that a related triangle

may have, to be part of the same plane that contains the selected triangle.

Edge Angle The Edge Angle-value defines which angle should be used to determine

edges of the part that cannot be removed. Triangles deviating less than this

angle will be grouped into the plane of the other triangles.

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Iterations You can choose how many triangle reduction iterations will be performed.

2.3. Wrap

The wrap function creates a wrapping surface of the selected entities. This tool is particularly

useful for medical parts, to filter small inclusions or close small holes. Furthermore, the

function is a useful tool towards Finite Element Analysis, where an enveloping surface is

needed.

Functions on Objects to Wrap





Show only selected

objects


Smallest Detail Corresponds to the size of the triangles on the newly created surface.

Closing Distance Determines the size of gaps that will be wrapped away via the operation.

Protect thin walls If this option is not selected, there is no protection of thin walls. Depending on

the smallest detail, it is possible that walls with a thickness within the same

range are collapsed.

If this option is selected, thin walls will be preserved. This means, however,

that the resulting model will be slightly thicker than the original, entirely

depending on the smallest detail parameter that is chosen.



CHAPTER 4: Pore Analysis The Pore Analysis module provides the necessary tools to completely characterize a porous

structure. Measurements frequently used in Tissue Engineering, including porosity, pore

interconnectivity, chamber pore size distribution, average pore diameter, throat pore size

distribution and specific surface area can easily be performed.


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1. Starting Pore Analysis Module The Pore Analysis dialog can be started in one of the following ways:

Via the Measurements toolbar:

Select the Pore Analysis button

Via the menus:

Select Analyze Pores from the Measurements menu.

Via the Project Management:

You can open the Pore Analysis dialog by selecting the New button of the Measurements

tab.

Note: If you're not able to start the Pore Analysis Module, you probably haven't entered the passwords yet. Go to Options > Licenses and fill in the correct passwords.

2. Performing a Pore Analysis In the Pore Analysis dialog, start with the selection of the 3D object in the Objects section.

Select the Measurements you want to perform on that object by checking the checkmarks.

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Porosity Defined as the void volume relative to the total volume (where the total

volume is approximated by the bounding box:

Average Pore diameter Defined as the average of the diameters of the largest non-

overlapping spheres that can fit in the pores

Pore interconnectivity Defined as the fraction of the void volume connected to the outside of

the object, relative to the total void volume.

Specific surface area

Chamber pore size distribution Describes, for each voxel, the largest overlapping spherical pore.

Throat pore size distribution Describes , for each voxel, the largest overlapping spherical pore,

where the sphere can move to the outside of the object

In Calculation indicate the voxel size as a value of discretization for your measurements and

click on Calculate to initialize the calculation of the selected measurements.

VolumeTotal

VolumeVoidPorosity

n

i

sizePoren

SizePore1

volumevoidTotal

outsidethetoconnectedVolumeVoidctivityInterconnePore

volumeTotal

areaSurfaceAreaSurfaceSpecific


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3. Checking Pore Analysis measurements The results of the Pore Analysis are listed in the Measurements tab in the Project

Management. Each measurement has its own information dialog, which can be visualized by

clicking in the Properties icon .

4. Exporting Pore Analysis measurements The results of the Pore Analysis can be exported as a text file. Select the action button in the

Measurements tab in the Project Management and select Export .txt. Select the

measurements you want to include in the text file and click Add.


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CHAPTER 5: MedCAD MedCAD is designed to make a bridge between medical imaging (CT and MR) and CAD

design. This means that it can export data from the imaging system to the CAD system and

vice versa.

Use the right tools in the right software.

MedCAD is not a design software. Many software packages are available to make designs

and most designers are already familiar with a certain CAD package. Learning yet another

CAD system would be a waste of time.

A CAD software is not an imaging software. If you try to convert all the medical data to your

CAD system, your system will slow down drastically. Not all the data from the images can be

converted to the CAD system: only a surface representation of the images is visible in the

CAD system.

Therefore it is better to make the interpretations on the images in MedCAD, taking into

account all the gray value information (soft tissue, different types of bone, tendons, etc.…).

On the images, basic features can be recognized and converted to geometrical entities (basic

axes, reference curves, anatomical landmarks). Only the surfaces which are needed to make

a fit are really converted to B-spline surfaces.

On the other hand, CAD design can be imported in the Mimics via the STL interface. The

designs are visualized in 2D sections together with the actual images, or in 3D shaded

representations, with the anatomical data in a transparent mode.

With this method, it is possible to bridge between the images and the CAD system in a few

minutes time.

1. Starting MedCAD All MedCAD functions are loaded immediately in Mimics after registration of the MedCAD

module. There is no specific way to start MedCAD. When the module is registered the extra

feature appears in the interface.

On the menu bar:

The MedCAD menu lists geometrical objects that can be drawn freely or fitted onto

polylines. It also allows you to fit freeform curves and surfaces on polylines.

In the Export menu:

Two new export file formats are added: Point Cloud and Iges.

In the Project Management:

Extra CAD Objects tab page.

Extra options are added to the action list of the Polylines tab: select a polyline-set and

click on the action button to fit a MedCAD object on the polylines or to export the polylines

as Iges.

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Note: If you're not able to start MedCAD, you probably haven't entered the passwords yet. Go to Options > Modules and fill in the correct passwords.

2. CAD Objects tab

2.1. List of created Objects

Name Name of the object. By clicking on the name of the object, it can be renamed.


2.2. Functions on Objects

New Creates a new Object. The object menu appears :


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Click on the desired object to go to the correct help page.

Delete Deletes the selected objects.

Properties Displays the properties of the selected object.

Locate Locates the selected MedCAD object

Action The action button lists all the available action on MedCAD objects. You can

generate a mask from a MedCAD object or export them as IGES

(International Graphics Exchange Standard) or as STL.

3. Exporting Iges files Different Iges export possibilities are available in MedCAD:

3.1. Starting from the Export menu:

By selecting Iges in the Export menu, a dialog is displayed where you can choose to export

the contours of a mask or a 3dd file as an Iges file. The entities used are of type 106 and form

12 (linear path entity).

The advantage of starting the Iges export from a mask is that you can create extra contours

(inter-layer) due to interpolation (see the “layer thickness” parameter on the RP Slice

calculation parameters page). The disadvantage is that all contours of your mask will be

exported. Although, there are filters available to filter out small contours and data points of

contours in order to reduce the file size.

Note: If you only want the contours of the mask, make sure the “layer thickness” parameter is set to the slice distance of the image set.

If you want to maintain the original position in space, make sure the First Layer height parameter is set to the first table position. (Otherwise the contours will be translated to this value)

3.2. Starting from the Polylines tab page:

By selecting a polylines set in the Polylines tab page of the Project management and by

clicking the Iges Export button, the selected polyline set is exported as an Iges file. The

entities used are of type 106 and form 12 (linear path entity).

The advantage of starting the Iges export from a polyline set is that only the contours of

interest are exported. The disadvantage is that interpolation between the contours (interlayer)

is not possible.

The same filters are available as in the RP Slice module.

3.3. Starting from the CAD Objects tab page:

By selecting one or more CAD objects in the CAD Objects tab page of the Project

management and by clicking the Iges Export button, the selected CAD Objects are exported

as one Iges file.

The entities used are:

Analytical Geometrical objects (sphere, line, plane, …): according the standard IGES

representation. For example, a sphere is exported as a circular arc revolved around an

axis.

Free form objects (Curves, Surfaces): NURBS representation.

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3.4. Starting from MedCAD menu:

By selecting Export all Objects to Iges in the MedCAD menu, all available CAD objects in

the project are exported as one Iges file. If you want separate Iges files for each CAD object,

use the Iges Export button in the CAD Objects tab page of the Project Management.

4. Exporting point cloud files By selecting Point Cloud in the Export menu, a dialog is displayed where you can choose to

export a 3D object as a Point Cloud file.

4.1. Description of the main areas

Select a 3D to export

in Point Cloud format

This area displays the 3D objects that are currently available in your project.

Select here the desired object to process.



directory structure. Select the location where you want your Point Cloud file

to be placed.

File name You can change the file name of your Point Cloud file.

Save as type At this time the only possible output format is ASCII.

5. MedCAD Menu

5.1. MedCAD Menu

This menu contains the following items:


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5.2. Polyline Growing

Starts the Polyline Growing mode. The Polyline Selector Toolbar appears:

The Polyline Growing tool provides the capacity to create several sets of polylines. The

operation can be performed on one single polyline or in 3D.

The parameters needed are:

From The set from where the polylines are grown

To The set to where the polylines are grown to. This can be an existing selection

or a new created one.

Correlation A measure for the strength of matching (%). This is done with a geometrical

comparison.

Auto multi-select This parameter can be turned on/off. If it is turned off only the current polyline

will be grown. If this parameter is turned on, all polylines according the

Matching parameter will be grown.

Keep Originals By default the polyline that is grown into a new set is removed from the

source set. You can choose to keep this polyline in the source set by

enabling the Keep Originals checkbox.

Selection is done on the images in 2D by drawing a rectangle (Press the left mouse button to

indicate a corner of the zoom rectangle, drag and release to indicate the opposite corner)

around the desired polyline, or simply by clicking on the desired polyline.

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If there is a polyline where the shape is a bit deformed, you can alter it by editing on your

segmentation mask. In the edit mode you will be able to update the polylines.

5.3. Point

5.3.1. Creating Points

There are two ways to create a point:

5.3.2. Draw

The cursor will change to . Simply click on the 2D images to create a point.

The point can be moved in the 2D images and 3D view by dragging it with the left mouse

button.

5.3.3. Keyboard

The following window appears:

Type in the X, Y, and Z coordinates of the point.

Click on the colored button in order to change the color of the MedCAD object.

5.3.4. Context menu


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Delete Deletes the selected point.

Hide Hides the selected point.

CAD Objects List Opens the CAD Objects tab page in the Project Management.

5.4. Line

There are three ways to create a Line:

5.4.1. Fit on Polylines

When creating an object based on a polyline set, the following window appears:

Select the desired polyline set to fit the object on and press OK.

5.4.2. Draw

The cursor will change to . Simply click a start and end point on the 2D images to

create a line (Start and end point can lie in different images)

The line can be moved in the 2D images by dragging the end points with the left mouse

button.

5.4.3. Keyboard


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Type in the X, Y, and Z coordinates of the start and end point of the line.


5.4.4. Context menu

Delete Deletes the selected line.

Hide Hides the selected line.

CAD Objects List Opens the Objects tab page in the Project Management.

5.5. Circle

There are three ways to create a circle:




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5.5.2. Draw

The cursor will change to . Simply click three points on the 2D images to create a circle.

Changing to another slice or to another 2D window is possible.

The circle can be moved in the 2D images by dragging its center point with the left mouse

button.

5.5.3. Keyboard


Type in the X, Y, and Z coordinates of the center point, followed by the direction: the

coordinates of the direction of the normal vector of the plane in which the circle is located.

Entering the radius fully determines the circle (see figure).


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5.5.4. Context menu

Delete Deletes the selected circle.

Hide Hides the selected circle.

5.6. Sphere

There are three ways to create a Sphere:




5.6.2. Draw

The cursor will change to . Simply click four points on the 2D images to create a sphere.

Changing to another slice or to another 2D window is possible.


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The sphere can be moved in the 2D images by dragging the control points with the left mouse

button.

5.6.3. Keyboard


Type in the X, Y, and Z coordinates of the center point and the radius.


5.6.4. Context menu

Delete Deletes the selected sphere.

Hide Hides the selected sphere.


5.7. Plane

There are three ways to create a Plane:



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5.7.2. Draw

The cursor will change to . Simply click three points on the 2D images to create a plane.

The plane can be moved in the 2D images by dragging the control points with the left mouse

button.

5.7.3. Keyboard


Type in the X, Y, and Z coordinates of a point which is part of the plane followed by the

coordinates of the normal vector of the plane.


Change the width and height of the plane to change the visualization in the 3D view of the

plane.

5.7.4. Context menu


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Delete Deletes the selected plane.

Hide Hides the selected plane.


5.8. Cylinder

There are three ways to create a cylinder:




5.8.2. Draw

The cursor will change to . Simply click a start and end point of the cylinder axis,

followed by a point which indicates the radius on the 2D images to create a cylinder (see

figure).

The cylinder can be moved and in the 2D images by dragging the control points with the left

mouse button.

256

5.8.3. Keyboard


Type in the X, Y, and Z coordinates of the start and end point of the cylinder axis, followed by

the radius of the cylinder.


5.8.4. Context menu

Delete Deletes the selected cylinder.

Hide Hides the selected cylinder.

5.9. Splines

There are two ways of creating a Spline:


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5.9.1. Fit On Polylines

Polyline Set Select the desired polyline set.

Set Check This area (under the Polyline Set selection) indicates if the polyline set is

valid for freeform curve generation.

Order The order of the polynomials used. Best values are either 3 or 4, e.g. an

order of 3 means that cubical polynomials are used.

Number of control points Control points can be seen like little magnets which attract the spline. The

more control points used, the better the fit will be. Some caution in increasing

the number of control points is advised. The basis of a spline is a polynomial

and a polynomial has the tendency to wave. So, if the number of points is too

high, the fit of the polyline will become worse.

Closed The spline can be closed or not.

5.9.2. Draw

When Draw Curve is selected the cursor changes to and the spline toolbox will appear

on the screen.

5.9.3. Spline toolbox

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a. Select spline

This function allows you to select the spline you want to edit. The points of a selected spline

are in white. The points of a non-selected spline have the same color as the lines of the spline.

The action you do is always performed on the selected spline.

b. Create spline

This function allows you to draw the spline. These are the steps to perform:

Indicate the path of the spline with the left mouse button; for every change in direction

along the nerve, you need to click once. In order to terminate the nerve, double click the

left mouse button or click the right mouse button.

While drawing the nerve you can scroll through the images with the cursor keys if needed.

Fine adjustments can be made by dragging the points to a new location. The spline can

be moved entirely by dragging the orange line.

c. Delete a spline

Select the spline you want to delete and click on the Delete nerve button.

d. Add point to spline

Click on the Add point to spline button, hover the mouse over the spline segment were you

want to add the point. The cursor will change into a pencil. Click your left mouse button to add

a point.

e. Remove point from spline

Click on the point of the spline you want to delete. The selected point will be colored green.

Click on the Remove point from spline button to delete the point.

f. Close spline

Click on this button to close the spline.

g. Spline properties

This button launches the Spline Properties dialog.

5.9.4. Spline Properties


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You can view the properties of a spline by clicking on the Properties button in the Project

Management, CAD Objects tab.

Here you can change the color, the diameter and the name of the spline. You can also find

some information about the order, length and the number of control points of the curve.

5.10. Freeform Surfaces

The only way to create a freeform surface is to fit it on a polyline set. The following window

appears:

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Polyline Set Select the desired polyline set.

Set Check This area (under the Polyline Set selection) indicates if the polyline set is

valid for surface generation.

Order The order of the polynomials used. Best values are either 3 or 4, e.g. an

order of 3 means that cubical polynomials are used.

Number of control points Control points can be seen like little magnets which attract the surface. The

more control points used, the better the fit will be. 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 of the polyline will become worse.

Closed The surface can be closed or not.

U en V parameters A parametric surface typically has 2 parameters: a u-parameter and a v-

parameter. These are the running coordinates in two in-plane orthogonal

directions. In MedCAD those two plane-directions are fixed. The u-parameter

runs perpendicular to the image plane. The v-parameter runs in the image

plane. For each parameter Order, Number of control points and Closed have

to be set.

Caution: a surface closed in two directions is NOT a cylinder closed on top

and bottom, but a torus.

5.10.1. Freeform Surface Info


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You can view the properties of a Freeform Surface by clicking on the Properties button in the

Project Management, CAD Objects tab.

Here you can change the color and the name of the surface. You can also find some

information about the order and the control points of the surface.

5.11. Freeform Tree

This tool allows you to calculate the centerline of a 3D object. These centerlines can be

exported together with a range of measurements.

Resolving resolution Select the minimum detail you want to resolve.

Number of iterations Sets the amount of iterations you want the algorithm to perform.

Distance between

control points

Sets the distance between two successive control points

5.11.1. Centerline properties

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Label

Name Name of the centerline.

Visualization

Centerline color Sets the color of the centerline.

Highlight color Sets the color of the highlighted branches of the centerline.

Show branching points Sets the visibility of the branching points on or off.

Branches

Name The name of the branch

Length(mm) Length of the branch

Visibility The visibility of a branch can be toggled by clicking on the sunglasses.

Group You can group branches together by selecting the branches segments you

want to include in the same set and clicking on Group, or simply by dragging

and dropping branch sets.

Delete Select a branch and click on delete to remove the branch from the list.

Export You can export the centerlines as Iges files or export the coordinates of the

centerlines and the measurements on the centerlines as Text file.

Export of centerline Properties


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Export

Output Directory Select the destination folder.

File Name Select the file name

Save as type The centerlines can be exported as Text or as Iges file.

The text file will list the position and measurement information of the control

points. The information is grouped per branch and is listed in columns, the

coordinates of the control points are indicated by Px, Py and Pz., the normal

are represented as Nx, Ny and Nz.

The Iges file exports the control points and the connection between them.

Besides the control points also the best fitted, minimal and maximal diameter

can be exported as an Iges file.

Measurements

Best fitted diameter Diameter of the best fit circle in a control point. The measurement is exported

as Dfit.

Minimal diameter Diameter of the inscribing circle in a control point. The measurement is

exported as Dmin.

Maximal diameter Diameter of the subscribing circle in a control point. The measurement is

exported as Dmax.

Curvature The coordinate and normal of the curvature point. This is the point of the

circle that determines the curvature for the segment that has a length as

indicated in the measurement interface and has the control point as a mid-

point. The coordinates of the curvature point are exported as Pcx, Pcy, Pcz,

the normals are indicated by Ncx, Ncy, Ncz and the radius that defines the

curvature is represented by Rc.

Hydraulic Diameter Hydraulic diameter in each control point. The Hydraulic diameter is exported

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as Dh.

Hydraulic Ratio Hydraulic ratio in a control point. The Hydraulic ratio is exported as Xh.

Circumference Perimeter of the surface in a control point. The measurement is exported as

Scf.

Sectional area Area of the sectional surface normal to the centerline. The measurement is

exported as Area.

5.11.2. Cut Centerline Ending

The Cut Centerline Ending tool allows you to cut the centerline endings, in order to obtain

adequate flat surfaces that can serve as inlet/outlet surfaces for CFD analyses.

You can cut the centerline by going to the CAD objects tab in the project management and

selecting the optimal orientation of your cutting plane.

Centerline with irregular endings Centerline with flat surfaces after Cut Centerline Ending tool

5.11.3. Centerline Measurements

A complete range of measurements can be made on the calculated centerline by clicking on

New in the Measurements project management tab:


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Centerline Best Fit Diameter Diameter of the best fit circle in a control point. The measurement is

exported as Dfit.

Centerline Minimal Diameter Diameter of the inscribing circle in a control point. The measurement is

exported as Dmin.

Centerline Maximal Diameter Diameter of the subscribing circle in a control point. The measurement is

exported as Dmax.

Centerline Curvature The coordinate and normal of the curvature point. This is the point of the

circle that determines the curvature for the segment that has a length as

indicated in the measurement interface and has the control point as a

mid-point. The coordinates of the curvature point are exported as Pcx,

Pcy, Pcz; the normals are indicated by Ncx, Ncy, Ncz and the radius that

defines the curvature is represented by Rc.

Centerline Tortuosity Tortuosity of the segment that has a length as indicated in the

measurement interface and the control point as a mid-point. The

tortuosity is exported as T.

Tortuosity = 1 - (linear distance / distance along the branch)

Centerline Hydraulic Diameter Hydraulic diameter in each control point. The hydraulic diameter is

exported as Dh.

Hydraulic diameter = (surface X-section) / (circumference X-section)

Centerline Hydraulic Ratio Hydraulic ration in a control point. The hydraulic ratio is exported as Xh.

Hydraulic ratio = (hydraulic diameter) / (subscribing diameter of X-

section)

Circumference Perimeter of the surface in a control point. The measurement is exported

as Scf.

Sectional area Area of the sectional surface normal to the centerline. The measurement

is exported as Area.

5.11.4. Edit centerline control points

You can edit the centerline by manipulating the position of the control points. Select edit

Centerline Control Points and indicate the control point you want to change. This control point

will turn green. Subsequently, indicate two control points that indicate the boundaries of the

admissible changes in the centerline. These two editing bounds are displayed in black. You

can then drag the selected control point to its final position until the centerline displays the

desired shape. Apply the changes by double-clicking, You can cancel the operation with the

Escape (Esc) key.

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5.12. Analyses

This option will start 3-matic and allow you to perform several analyses on your 3D objects.

The analyses available include Wall Thickness, Curvature, Part Comparison, Distance to

Curve and Distance to Curve over Surface and Midplane Surface Analyses. You can perform

segmentation based on these analyses and export the information in a .txt file.

For more information on the analyses, consult the 3-matic Reference Guide.

5.13. Export all object to IGES

When "Export all objects to IGES ..." is selected, all created objects (spheres, freeform

surfaces, ...) will be exported to one iges file. The name of this file can be given in the dialog

box that will be displayed.

If however you want to created separate IGES files for every object, use the IGES button in

Project Management, CAD Objects Tab.


267

CHAPTER 6: FEA/CFD The Mimics FEA Module enables you to link from scanned images to Finite Element Analysis

(FEA) and Computational Fluid Dynamics (CFD) by exporting the files in the appropriate file

format. You can calculate 3D objects based on the scanned images and prepare these

surface meshes for Finite Element Analysis purposes. The Remesher in the FEA Module

assures that you'll end up with the most optimal input for the pre-processor of your FEA

software.

After converting the surface mesh to a volume mesh in the pre-processor, the volume mesh

can be imported in Mimics again. Materials can then be assigned to the volume mesh, based

on the Hounsfield Units in the scanned images or on the segmentation of the project.

1. Starting the FEA/CFD module All FEA functions are loaded immediately in Mimics after registration of the FEA module.

When the module is registered, a few extra items are visible in the interface:

On the FEA/CFD menu:

An extra FEA menu, listing the different FEA functions.

In the Export menu, new export file formats are added: Abaqus, Ansys, Patran neutral,

Fluent, Nastran and Comsol.


Extra FEA Mesh tab.

Extra buttons on the 3D Objects tab and the STLs tab: select a 3D Object or STL and

click on the Remesh button to open 3-matic.

Note: If you're not able to start the FEA module, you probably have not entered the passwords yet. Go to Options > Licenses and fill in the correct passwords.

268

2. FEA Mesh tab

2.1. List of created Objects


Visible Lists if the object is visible or not by means of glasses. You can change the

visibility by clicking on the glasses.

Material Lists if the material assignment is visible or not by means of glasses. You can

display or hide the material assignment by clicking on the glasses.

Note: If you haven't assigned any materials to a FEA mesh, you will not be

able to make the material assignment visible.

Contour Visible Lists if the contours of the volume mesh are visible in the 2D images or not by

means of glasses. You can display or hide the contours by clicking on the

glasses.

2.2. Functions on Objects

Import Imports a volumetric mesh. For more information about the import process,

please refer to the Import help page.

Copy Copies the selected volume mesh to the clipboard. The volume mesh can then

be pasted into a 3-matic project or another Mimics project.


Properties Displays the properties of the selected object:


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Duplicate Duplicates the selected FEA mesh

Remesh Opens the Mimics Remesher, where you can calculate the quality of the

volume mesh, convert tet-4 to tet-10 and vice-versa and extract the surface

from the volume mesh.

Material Calls the window to do a material assignment for the selected object.

Export Exports the selected object to a Patran neutral, Ansys, Abaqus or Fluent file.

3. FEA Menu

3.1. FEA menu

When the FEA module is licensed, the FEA menu appears in the menu bar. This menu lists

the different features of the FEA module:

3.2. Calculate Non-Manifold

Allows you to automatically calculate a non-manifold assembly of complex structures directly

from mask. You can select a specific number of masks from the list and indicate the ones that

belong to the assembly. The parameters can be adjusted by clicking on the Options button.

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3.3. Remesh

Allows you to select a 3D object or an STL that will be remeshed. You can select one or more

3D objects or STLs out of the list. When you click on the OK button, the remesher will

automatically be started with the selected object already loaded.

3.4. Create mesh

This operation allows you to create a volume mesh based on voxels.


271

3.4.1. Listed masks

Here the created masks are listed. Select the masks from which you want to create a volume

mesh.

Note: You cannot calculate a volume mesh for an empty mask

3.4.2. Element type

You can choose to create a volume meshed consisting out of Hexahedral or tetrahedral

elements.

3.4.3. Filtering

Close small holes: Closes small holes.

Filter small parts: Removes small loose parts.

Improve connectivity: Increases the connectivity to neighboring elements.

3.4.4. Smoothing

This operation allows decreasing the sharp edges of the voxels. It gives the best results when

the voxels are more or less cubic.

Smoothing iteration count: Defines how many times the program should make the

calculations.

Smoothing factor: Strength of smoothing – higher values give better smoothing but will

change geometry more than smaller ones.

Volume compensation: This feature compensates the shrinkage process associated to the

smoothing operation.

3.4.5. Voxel grouping

272

This option allows grouping of voxels to calculate the volume mesh. The reduction is given

relative to the X-size (= Y-size) of a pixel in the image and relative to the height (Z-size) of a

pixel in the 3D data set.



An XY- or Z-resolution of 1 means no voxel reduction in the plan or the Z-direction.

Apply filtering on grouped voxels: by enabling this option the filters will be applied on the

grouped voxels instead of the original ones.

3.4.6. Estimated number of elements

Shows the amount of elements that will be created.

3.5. Material

Allows you to select a FEA mesh out of the list for which you want to assign materials. When

you have selected the correct mesh and click on the OK button, the material assignment

window will be opened for the selected mesh.

3.6. Import

Allows you to browse for a volumetric mesh. When you have selected the right file and click

on the Open button, the volumetric mesh will be loaded and listed in the FEA mesh tab.

You can import Patran neutral, Ansys and Abaqus volumetric meshes. For more information

about which elements are supported please read the Supported Files page.


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3.7. Export

Allows you to export a 3D object, a STL or a FEA mesh to a Patran Neutral, Abaqus, Ansys,

Fluent or Nastran file. In the case of a FEA mesh, both the mesh and the material assignment

(if available) will be exported.

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Note: FEA meshes can also be exported to a colored STL file. These colored STL files are invalid STL files and should only be used for visualization purposes! The colored STL file could for instance be used to view the material assignment inside the volumetric mesh.

4. Calculate Non-Manifold The calculate non-manifold function tool ensures that a common border is calculated for

adjacent masks. This results in an immediate non-manifold assembly for the different

materials in the dataset, allowing a straightforward workflow towards FEA. This function is

particularly suitable for complex structures composed of irregular contacts, namely

composites, cortical and trabecular bone, bone and cartilage, etc.

The first step for creating a non-manifold assembly is the segmentation of the different

materials of the objects being selected. Once the masks are created, add the mask to the

assembly by clicking on the space under the Assembly column.

Note: The first mask that is added to the assembly will remain unchangeable. When you add a second mask to the assembly that intersects with the firstly added mask, the intersecting regions will be substituted from the last mask added to the assembly.


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In the FEA/CFD menu select the Create Non-Manifold function. The Calculate 3D dialog will

pop-up.

If you click on the Options button, the following dialog pops up:

276

All the parameters present in this dialog correspond to the parameters present in the

Calculate 3D dialog, with the exception of the Accuracy field. The accuracy sliding bar is a

scale between 0 and 100, where 0 corresponds to the lowest accuracy for the 3D object

calculation, but to the highest triangle quality of the mesh. Reversely, 100 corresponds to the

highest accuracy for 3D object calculation, but the lowest triangle quality. The higher the

triangle quality, the easier will be the remeshing process towards a volume mesh generation,

although the accuracy may be affected.

Note: For more information concerning the other parameters, consult the Help pages under Calculate 3D.

Once the parameters are defined, select OK and Calculate. A perfect non-manifold assembly

is added to the 3D objects list.


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5. Remeshing A STL or 3D object can be remeshed using the Remesh module. This is needed in order to

raise the quality of the triangles so that a tetrahedral mesh can be built from them.

There are some steps you can do to make sure that your 3D object that is calculated in

Mimics to make sure that the remeshing will go smoothly:

When calculating a 3D in Mimics, you can do a shell reduction so that small shells are

removed. If you go to the Segmentation Menu and choose Calculate 3D and then Options.

In that dialog you can choose to do a Shell reduction with value 1.

It is also interesting to fill as much holes as possible. You can use the Fill Cavity from

Polyline tool to remove holes from your 3D object or use the Wrap function in the

Remesher.

Most FEA packages don't like small details. Thanks to the morphology operation in

Mimics, you can already smooth out small details on the surface.

5.1. Remeshing Protocol

Below you can find a basic remeshing protocol. These are the steps that are normally taken

to make sure the mesh is optimal for FEA purposes. The different parameters for each step

are dependent on each dataset and won't be given in this basic protocol, but an example of

the application of this protocol can be found in Tutorial Case 8.

STEP A: Check if the 3D object doesn‟t have thin walls or structures that will be hard to

model but are of no importance for your FE Analysis. You can use the Wrap function to

create a closed enveloping surface around your part and remove all the small inclusions that

may have resulted from the segmentation.

STEP B: Depending on the parameters you‟ve selected for 3D calculation, the resulting 3D

object may include too much detail. As a first step you can do a defeaturing on the 3D object

therefore select the Smooth button from the Fixing toolbar. Next apply Reduce to

reduce the number of triangles using a large angle value.

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STEP C: Check the size of the triangles. To do this, create an inspection scene by selecting

your object and clicking on .Select from the inspection measure dropdown box Smallest

edge length (A).

In the histogram, select as current measure the Inspection measure and check the mean

value of the smallest edge length. Do exactly the same for the largest edge length.

Remember or write down these values.

STEP D: When you notice in the inspection diagram that there are still too many small

triangles, you can filter them out with the Filter Small Edges button which can be found

in the Fixing toolbar.

STEP E: After you‟ve reduced the amount of triangles you can optimize your mesh with the

Auto Remesh tool. First select the desired quality parameter from the quality Shape

measure dropdown box. Typically for FE analysis the Height/Based (N) parameter is used,

while for CFD the Skewness (N) parameter is used. With the Auto Remesh function, a quality

threshold of 0.3 to 0.4 can be achieved.

STEP F: You can now reduce the amount of triangles preserving the achieved quality with the

Quality Preserving Reduce Triangles function.

STEP G: In some cases there are still some low-quality triangles left at this point (you should

not have started any local operations already). They are usually removed by another call to

the split-based algorithm (with larger geometric error than before).

STEP H: If low-quality triangles still persist, use local operations to fix them.

STEP I: Make the mesh more uniform by doing several calls to the Quality Preserving

Reduce Triangles with increasing geometric error. Stop when both the mesh looks uniform

enough and the total number of triangles is small enough.

STEP J: Call the self-intersection test with the Mark Intersecting Triangles tool and fix them

by deleting the appropriate triangles and filling the resulting hole.

STEP K: If small triangles persist and you do not want to increase the geometrical error any

further, use the grouping around 'smallest edge length' to collapse them manually.

STEP L: Check and remove sharp geometry using the sharp geometry measures (sharp

geometry, peaks, shafts) which can be found in the inspection measures. You can do this

step based on intuition or on the feedback from the created volume mesh quality from your

FEA-preprocessor.


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STEP M: If needed you can control the growth of your triangles with the Growth Control tool

.

STEP N: If steps G, H and/or I introduced low-quality triangles call the Auto Remesh

algorithm again.

STEP O: Check if there are large triangles compared to the local wall thickness by using the

inspection measure Wall thickness/Edge length (A). You should have at least 4 elements in a

wall for CFD applications and minimum of 1 or 2 elements for FE analysis.

STEP P: Create Volume Mesh by clicking on the corresponding icon . Select the

method you want to use for the calculation and specify the maximum edge length as having

the same value as specified for the Auto remesh tool (if applicable). In case you are working

with non-manifold assemblies created directly from masks, you can group the sub-volumes

according to the original mask. This means that each sub-volume will correspond to one

material, allowing a straightforward process during material assignment. Select the preferred

shape measure and specify the shape quality threshold desired for your volume mesh.

STEP Q: Analyze Mesh Quality by clicking on the icon . Select the checkbox for

Analyze volume mesh and select the adequate shape measure. Indicate the shape quality

threshold value and specify the histogram interval for your analysis. In case you want to

visualize the surface triangles in the area of the bad elements, select Mark bad triangles and

specify the element growth.

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STEP R: In case you have some low quality elements, go back to STEP I and remesh your

surface mesh. Repeat the steps O and P until you obtain a volume mesh with the desired

quality.

STEP S: If your volume mesh has an adequate quality for your FE analysis, close the

Remesher and export your mesh with the desired file format.

For more information on each of the above-mentioned tools, consult the 3-matic Reference

Guide.

6. Material Assignment You can assign materials to FEA meshes via the FEA/CFD menu or the FEA mesh tab.

Before you can assign materials to the elements of the volumetric mesh, Mimics will first

calculate a gray value for each element of each sub-volume of the mesh. This gray value will

then be used in further calculations. Mimics uses an accurate method to assign gray values to

elements by calculating exact intersections between voxels. While being accurate, care has

been taken that the calculations can be performed efficiently.

The gray value assignment is stored in the Mimics project file, so the gray value calculation

only needs to take place once for each volume mesh in a Mimics project, no matter how many

different material assignments are exported.

After the calculation of the gray values of the elements of the volumetric mesh, the material

assignment window will appear:


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In the Sub-volumes list, the different volumes of a non-manifold assembly will be displayed,

together with the number of volume elements. You can select the option Select all sub-

volumes in case you want to perform the material assignment for the complete volume mesh.

In case you want to assign material properties simply in a specific number of volumes, then

you can indicate them in the list.

In the Elements Histogram, Mimics will show for each gray value the amount of elements that

were assigned that particular value. After the grey value calculation, each element has its own

gray value based on the image data set. Two methods can be used to convert this gray value

into material properties: Uniform Method and Look-up File Method. A first step that is taken

for both methods is discretization: the range of all gray values is subdivided into intervals.

How this discretization is done depends on the chosen method.

The third option to create materials is the Mask Method. During the calculation of the

grayvalue of each element, also the volume of intersection with the different masks in the

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project is calculated. Each element is assigned to one mask based on this volume of

intersection. For each material the properties can then be defined in the material editor.

6.1. Material assignment method

6.1.1. Uniform method

In the uniform method, the discretization of the gray values is done by dividing the range of

gray values that occur in the volume mesh into a specified number of equal sized intervals

that each represents a material. The center gray value of each interval is chosen as a

representative for that interval. After you have entered the amount of materials in the edit box,

you can apply the material assignment, by clicking on the OK button.

The color of the elements will be determined according to following color scale:


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6.1.2. Look-up File Method

For this method a look-up file is specified that indicates which intervals are used to divide the

range of gray values (look-up files can also be expressed in Hounsfield units). Each interval

can be assigned a specific density value. A lookup file can be chosen by clicking on the Load

button. It is possible to call the default viewer or editor for the specified look-up file by clicking

on the Open with button.

The color of the elements will be determined according to following color scale:

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The format of the lookup table is very simple. The first line specifies the xml format of the file.

In the header of the xml file, the version of the file can be specified (1.0 for the moment).

Ranges of grayvalues are specified by their first boundary in the Start tag. The Density tag

specifies the density that should be associated with the material.

Example: <?xml version="1.0" encoding="UTF-8"?>

<LookupTable>

<Header>

<Version>

<Major>1</Major>

<Minor>0</Minor>

</Version>


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<Units>Hounsfield</Units>

</Header>

<Table>

<Interval><Start> 0.0e0 </Start><Density> 0.0e0 </Density></Interval>



</Table>

</LookupTable>

This Lookup file specifies 3 materials:

Material 1 contains all elements with HU (Hounsfield Unit) between 0 and 300. That

material is assigned a density of 0

Material 2 contains all elements with HU between 300 and 600. That material is assigned

a density of 300

Material 3 contains all elements with HU between 600 and 3071. (HU is maximal 3071).

That material is assigned a density of 600

Note: You can choose between "Hounsfield" or "Grayvalue" as the Unit type.

Remark: The Limit to Mask option 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.

6.1.3. Mask Method

By using the material assignment from mask, you can use the segmentation in your project to

assign materials to your elements. For each used mask, one material will be created. For

each element one of the materials is assigned based on the volume of intersection of that

element with each mask. If there are elements in the volume mesh that fall completely outside

the selected masks, one extra material is created for those elements. If an element has the

same intersection volume with several masks, the first mask in the list is used for assigning a

material to that element.

When choosing the mask method, click on the Select button to select which masks you want

to use:

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After this you can see the assignment of the materials in the histogram:

Note: If you change one of the masks after doing the grayvalue calculation and choose to do a material assignment from masks, Mimics will have to calculate the grayvalues again.

6.2. Material Expressions

6.2.1. Density Expression

The density expression can be used for translating the grayvalue of an element to a density

when using the uniform method.

To do this, an empirical expression of the form A+B*X^C+D*X^E can be entered to convert

the gray value into a density value. This method can also be used to export gray values: if

0+1*X^1 + 0*X^1 is used as a density expression, the representatives of each interval are

written out as densities.


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Note: For the look-up method, the density for each material is taken from the look-up file. For the mask method you have to enter the density for each material yourself in the material editor.

6.2.2. E-Modulus expression

Based on the density value, an expression can be entered to define the e-modulus for each

material. The entered expression will only be used if the checkmark is enabled. If there is no

density value available for a certain element, the e-modulus value will also remain empty.

6.2.3. Poisson expression

Based on the density value, an expression can be entered to define the poisson coefficient for

each material. The entered expression will only be used if the checkmark is enabled. If there

is no density value available for a certain element, the poisson coefficient value will also

remain empty.

6.3. Material Editor

The assigned materials and their properties can be displayed and adjusted in the material

editor. You can change the value of one of the fields by clicking on the value. You can also

adjust multiple values at the same time by selecting them and filling in a new value.

Fields that are empty in the material editor will either not be exported or will receive a value of

0 depending on the export format.

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The color of each material can be changed by double-clicking on the color box:

Note: About units (Hounsfield units/Gray values): Hounsfield units are the unit image data that comes from medical scanning devices. Grayvalues are the unit that is used internally in Mimics. Both units relate as value in GV = value in HU + 1024. Mimics has a preference setting to select which unit is used in the user interface (Options -> Preferences -> General -> Pixel Unit). Warning: the current unit is also used for the density expression.

Note: Most FEA software do not allow you to enter a density with a negative value, so make sure you choose your expression accordingly or adjust the values manually in the material editor.

7. Using Mimics with Patran

7.1. Export a volumetric file to Patran

After you have created a volume mesh of adequate quality for FEA purposes and performed

the material assignment, you can export it to a neutral Patran file. To do this, go to the Export

menu and choose Patran. This will open the following dialog:


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Select the volume mesh you want to export and click on the Add button. Make sure the

Output Format is Neutral Files (.out) and press OK.

7.2. Export a surface file to Patran

If you want to create your volume mesh using Patran, you can export your surface mesh as a

neutral Patran file. To do this, go to the Export menu and choose Patran. This will open the

following interface:

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You can export a 3D Object or an STL file to a Patran neutral file, by adding the object to the

list, choosing the Neutral File format and clicking on the OK button.

7.3. Import a mesh in Patran

The exported surface or volume mesh can be imported in Patran by going to the File menu

and choosing Import. This will open the following dialog:

Make sure you use the same settings as above.

7.3.1. Convert a surface mesh to a volumetric mesh

If you start with a surface mesh, choose the Elements button in the toolbar and choose to

create a solid mesh. Select a Tetmesh with Tet4 or Tet10 elements. Have a look at the

settings below how to do this:


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Next, choose to select triangles and select all triangles in the mesh. After clicking on the

Apply button, a volume mesh will be generated.

7.4. Export the volume mesh from Patran

You can export your volume mesh by going to the File menu and choosing Export.

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7.5. Import the Patran volume mesh in Mimics

You can import a Patran neutral file by clicking on the Import button in the FEA project

management tab:

This will open a file chooser:

Change the type of the listed files to Patran Neutral and all Patran files will be shown. Then

browse to the directory where the files are located, select the correct file and click on the

Open button, the files will be imported.

7.5.1. Supported element types

The Mimics FEA module supports four types of Patran elements:

5 (4-node tetrahedron)

7 (6-node wedge)

8 (8-node hexahedron)

5 (10-node quadratic tetrahedron)

Remark: If you require other element types, please let us know and we will try to implement those elements in our future releases.


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7.5.2. Supported Patran packets

The Mimics FEA module supports 6 Patran packets:

25 (File title)

26 (Summary data)

1 (Node data)

2 (Element data)

3 (Material properties, export only)

4 (Element properties, export only)

Material properties: Patran writes out 96 material properties. Mimics assigns only 7 of them,

the others are set to 0. Exported material properties: 2 (density), 27-29 (E-modulus), 30-32

(Poisson coefficient). For E-modulus and Poisson coefficient all three properties contain the

same value.

8. Using Mimics with ABAQUS

8.1. Export an ABAQUS volume mesh

You can export an ABAQUS volume mesh by going to the Export menu and choosing

ABAQUS. In the following interface you can then add your volumetric mesh and export it as

an ABAQUS file.

8.1.1. Export an ABAQUS surface mesh

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If you want to create your volume mesh using ABAQUS, you can export your surface mesh as

an ABAQUS file. To do this, go to the Export menu and choose Abaqus. This will open the

following dialog:

Add the 3D objects or STL files that you want to export, set the output format as Abaqus Files

(.inp) and press OK.

8.2. Import a mesh in ABAQUS

In ABAQUS/CAE, go to File -> Import -> Model. Browse to the directory where you have

saved your volume or surface mesh and select to import it.


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8.2.1. Convert a surface mesh to a volumetric mesh

In case you imported your surface mesh and you want to convert it to a volume mesh, choose

one of the following workflows, according to the version of ABAQUS you have:

a. Conversion in ABAQUS 6.4:

Switch to the Part Module and choose to Edit the Mesh.

This will open following dialog:

After choosing the Conversion of Tri to tet, click on OK and the surface mesh will be

converted to a volume mesh.

b. Conversion in ABAQUS 6.5

In ABAQUS 6.5 you should go to the Mesh module, choose the Mesh menu and the Edit ...

option. Then again choose to convert your mesh from tri to tet.

8.3. Export the volume mesh from ABAQUS

After the conversion of the mesh you can export your volume mesh by going to the Job

Module and choose to Create a Job.

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After choosing a name for your Job and choosing the correct model, click on Continue.


Choose to use the default settings and click on OK. After this a Job is created for your model.

Then you can go to the Job menu and choose the Write Input option to export an .inp file.


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8.4. Import the ABAQUS volume mesh in Mimics

You can import an ABAQUS volume mesh by clicking on the Import button in the FEA

project management tab:


Change the type of the listed files from Patran Neutral to ABAQUS File and all ABAQUS files

will be shown.

Then browse to the directory where the files are located, select the correct file and click on

the Open button. The files will be imported.

8.5. The ABAQUS file

There are some limitations for the format of the ABAQUS file. The structure of the file should

be:

*HEADING

*NODE

1, 432.3656005859375, -245.597900390625, 54.94200134277344

2, 347.5975952148438, -158.1038970947266, 4.51170015335083

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…

*ELEMENT, elset=region0, type=C3D4

474604, 14874, 14869, 14873, 14872

474605, 14874, 14868, 14870, 14869

…

Three important rules to follow are:

The commands *HEADING, *NODE and *ELEMENT should be written in capitals.

The commands *HEADING and *NODE should not have any text or spaces behind them.

There should be an empty line between the *HEADING section and the *NODE command

and between the *NODE section and the *ELEMENT command and after the *ELEMENT

section.

8.5.1. Supported element types

The Mimics FEA module supports four types of ABAQUS elements:

C3D4 (4-node linear tetrahedron)

C3D6 (6-node linear triangular prism)

C3D8 (8-node linear brick)

C3D10 (10-node quadratic tetrahedron)

Remark: If you require other elements types, please let us know and we will try implement those elements in our future releases.

8.5.2. Supported ABAQUS commands

The Mimics FEA module supports 5 ABAQUS commands:

*HEADING

*NODE

*ELEMENT

*SOLID SECTION

*MATERIAL

The *SOLID SECTION and the *MATERIAL command are only used during export and are

ignored during import.

The *ELEMENT command:

*ELEMENT, TYPE=<type>, ELSET=<name>

The *SOLID SECTION command:

*SOLID SECTION, ELSET=<name>, MATERIAL=<name>

The *MATERIAL command:

*MATERIAL, NAME=<name>

*DENSITY

<material density>

*ELASTIC

<E-modulus>, <Poisson>


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9. Using Mimics with Ansys

9.1. Export a volumetric file to Ansys

After you have calculated a volume mesh suitable for FEA purposes, you can export this

mesh to an Ansys file. To do this, go to the Export menu and choose Ansys. This will open


Select your volume mesh to be exported, set your Output Format as Ansys Preprocessor files

and click on the OK button.

9.1.1. Export a surface file to Ansys

If you want to create a volume mesh in Ansys, starting from a surface mesh created in Mimics,

you can export this surface mesh as an Ansys file. To do this, go to the Export menu and

choose Ansys. This will open following interface:

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Mimics can export your remeshed 3D object to Ansys as an Area-based or an Element-based

file:

Element-based: The part is exported as a mesh, having triangles as elements. To

generate the volume mesh in Ansys, the FVMESH command should be used.

Area-based: Each triangle is exported as a separate face into the Ansys-file. Importing

this file in Ansys will result in a remeshing of the file, and will lose the original triangulation.

We advise you to use the Element-based export as this will preserve the obtained quality of

the mesh. To export add the object to the list, choose the appropriate Ansys File format and

click on the OK button.

9.2. Import a mesh in Ansys

Your volume or surface mesh can be imported in Ansys by going to the File menu in Ansys

and choosing Read Input From.


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9.2.1. Convert an Element Based surface mesh to a volumetric mesh

In Ansys select File | Read input from and load the file

The surface element type is Shell93 by default.

Note: If desired you can change the surface element type with the command ET, ITYPE, Ename, KOP1, KOP2, KOP3, KOP4, KOP5, KOP6, INOPR (e.g. et,1,Mesh200)

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Add a solid element type to generate your volumetric mesh, you can again do this with the ET

command e.g. ET,2,SOLID92. Or in the main menu select Preprocessor | Element type |

Add/Edit/delete and add a solid element type.

If you want to load your volume mesh back into Mimics for material assignment you should

use one of the following element types:

SOLID72, SOLID185 (linear tetrahedron)

SOLID92, SOLID187 (quadratic tetrahedron)

SOLID185 (linear hexahedron)

If you require other elements types, please let us know and we will try implement those

elements in our future releases.

To generate the volume mesh you should use the command FVMesh or you can execute this

command from the main menu Preprocessor | Meshing | Mesh | Tet Mesh From | Area

Elements.

9.2.2. Convert an Area Based surface mesh to a volumetric mesh

First select an element type to which you want to assign the surface mesh. You can do this

with the ET command e.g. ET,1,SHELL93. Or in the main menu select Preprocessor |

Element type | Add/Edit/delete and add a surface element type.

To mesh the areas to elements, go to Main Menu > Preprocessor > Meshing > MeshTool.

In the MeshTool check smart size and put it to coarse. Select as mesh Areas and as Shape

Tri and free.


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Click on Mesh, the Mesh areas dialog pops up. In this dialog click on pick all.

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To release all associations between the current solid model and finite element model, execute

the command, MODMSH,detach.

Add a solid element type to generate your volumetric mesh, you can do this with the ET

command e.g. ET,2,SOLID92. Or in the main menu select Preprocessor | Element type |

Add/Edit/delete and add a solid element type.

If you want to load your volume mesh back into Mimics for material assignment you should

use one of the following element types:

SOLID72 (linear tetrahedron)

SOLID92 (quadratic tetrahedron)

If you require other elements types, please let us know and we will try to implement those


To generate the volume mesh you should use the command FVMesh or you can execute this

command from the main menu Preprocessor | Meshing | Mesh | Tet Mesh From | Area

Elements.

9.3. Export the volume mesh from Ansys

You can export the nodes of the volume mesh by going to the main menu Modeling | Create

| Nodes | Write Nodes. To export the elements select Elements | Write Elements.

9.4. Import an e volume mesh in Mimics

To import these files, click on the Import button in the FEA project management tab:


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Change the type of the listed files from Patran Neutral to Ansys File and all files will be shown

(Ansys files do not have a general extension).

Then browse to the directory where the files are located, select the nodes or the elements file

and click on the Open button. The import Ansys dialog is shown:

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Note: element and nodes file can be large. Please allow some time for the dialog to show up.

Browse to the remaining file. The minimal and maximum index will be filled. Also select the

type of elements of which the volume mesh consists out.

Instead of importing a nodes or elements file you can as well create a prep7 file and use it to

import the volume mesh.

9.5. The PREP7 file

The Ansys PREP7 file contains references to the nodes and elements files and material

property definitions. An example of such a file (without material properties) can be found

below:

/PREP7

ET,2,SOLID92

NRRANG,1,26407,1

NREAD,'AnsysTest_nodes_file',' ',' '

ERRANG,1,17317,1

EREAD,'AnsysTest_elements_file',' ',' '

This PREP7 file should be created manually. The easiest way is to copy the text to a new file

and adapt it to your needs.

/PREP7

This command indicates to Mimics that the file is a PREP7 file

ET,2,SOLID92

The first parameter (2) is the local element type and depends on your Ansys project. The

second parameter (SOLID92) is the type of the elements that is used in the mesh

NRRANG,1,26407,1

The first parameter (1) is the index of the first node and will be 1 in most cases. The second

parameter (26407) should be equal to the maximum node number. The third parameter (1) is

the increment of the indices of the nodes and will be 1 in most cases.


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These parameters can be derived from the Node status. The node status dialog is evoked by

executing the following commands:

NODES

STAT

The nodes status lists the maximum node number and the number of nodes defined. The

index of the first node is equal to the maximum node number minus the number of nodes

defined plus 1.

(index of first node =maximum node number - number of nodes defined + 1)

NREAD,'AnsysTest_nodes_file',' ',' '

The first parameter (AnsysTest_nodes_file) is the filename of the nodes file. The second

parameter ( ) is the extension of the file (we suggest not to use an extension). The third

parameter ( ) is the directory the file was written out to (we suggest to not use a directory)

ERRANG,1, 17317,1

The first parameter (1) is the index of the first node and will be 1 in most cases. The second

parameter (17317) should be equal to the maximum element number. The third parameter (1)

is the increment of the indices of the elements and will be 1 in most cases.

These parameters can be derived from the element status. The element status dialog is

evoked by executing the following commands:

ELEM

STAT

The element status lists the maximum element number and the number of elements defined.

The index of the first node is equal to the maximum element number minus the number of

elements defined plus 1.

(index of first element =maximum element number - number of elements defined + 1)

EREAD,'AnsysTest_elements_file',' ',' '

The first parameter (AnsysTest_elements_file) is the filename of the elements file. The

second parameter ( ) is the extension of the file (we suggest not to use an extension). The

third parameter ( ) is the directory the file was written out to (we suggest to not use a

directory)

9.6. The nodes file

The nodes file contains the coordinates for all nodes. The file can be written out in Ansys by

going to: Main Menu > Preprocessor > Modeling > Create > Nodes > Write Node File.

You can also write out the nodes file with following command:

NWRITE, Fname, Ext, Dir, KAPPND

With parameters:

Fname: File name (32 characters maximum)

Ext: File name extension (8 characters maximum)

Dir: Directory name (64 characters maximum)

KAPPND: Append key:

0 - Rewind file before the write operation

1 - Append data to the end of the existing file

Note: We suggest to write out the nodes file without an extension.

9.7. The elements file

The elements file contains the definitions for all elements. It‟s strongly advised to write out the

elements file in the LONG format. The file should be written out with following command:

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EWRITE, Fname, Ext, Dir, KAPPND, Format

With parameters:

Fname: File name (32 characters maximum)

Ext: File name extension (8 characters maximum)

Dir: Directory name (64 characters maximum)

KAPPND: Append key:

0 - Rewind file before the write operation

1 - Append data to the end of the existing file

Format: Format key:

SHORT - I6 format (the default)

LONG1 - I8 format

Note: We suggest to write out the elements file without an extension.

Note: We suggest to write out the elements file in the LONG format. If you have more than 99.999 nodes, you have to write out in the LONG format or Mimics will refuse to import the files.

9.8. Supported element types

The Mimics FEA module supports two types of elements:

SOLID72 (linear tetrahedron)

SOLID92 (quadratic tetrahedron)

If you require other elements types, please let us know and we will try implement those


9.9. Supported material properties

The Mimics FEA module supports three types of material properties:

DENS (Density)

EX (E-Modulus)

PRXY (Poisson coefficient)

9.10. Supported PREP7 commands

The Mimics FEA module supports 6 PREP7 commands:

ET

MP

NRRANG

NREAD

ERRANG

EREAD

The ET command:

ET,<local type element number>,<type>

The NRRANG/ERRANG commands:

NRRANG,<min>,<max>,<increment>

The NREAD/EREAD commands:

NREAD,<filename>,<file extension>,<drive+directory>

The MP command:

MP,<material property>,<material reference number>,<value>


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10. Using Mimics with Ansys Workbench The volume meshes created into Mimics can immediately be imported into Ansys workbench.

If you want to export multi-parts, you should first create a non-manifold assembly. More

information on how to create a non-manifold assembly can be found in the non-manifold

assembly tutorial.

10.1. Export to Ansys workbench

When you obtain your volume mesh go to the Export menu and choose Ansys. This will open


Select your volume mesh to be exported, set your Output Format as Ansys Preprocessor files,

click Add and click on the OK button.

10.2. Import in Ansys workbench

Open Ansys workbench and drag the Finite Element Modeler component system to your

project schematic.

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Right click on Model, select Add Input Mesh, and select browse to your Ansys APDL Input

mesh (*.cdb) file. Click open.


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This would load your mesh defined created in Mimics in Ansys workbench. In the workbench,

right click on Model and click on Edit to open the Finite Element Modeler window you‟re your

volume mesh. You can ignore any messages that may appear.

For simpler geometries it is sometimes better to use the automatic geometry creation tool.

However, here we will demonstrate how you can choose a region and assign boundary

conditions on them. Select a few element faces using the “Select Element Faces” option

and create components.

Right click on your selection and click on Add component option to save this surface for

defining boundary conditions later. This surface will be used to apply load. We will add

another surface component as fixity at the bottom of the femur as shown below.

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Close the Finite Element Modeler window to save your data and move to next step in the

analysis.

Add your analysis type by dragging one of the analysis systems to your project schematic

window. Drag the model from Finite element modeler cell to the model of your analysis

system to share the model data. This is shown below with a static structural cell. Update your

project by clicking on Update Project button.


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Double click on the Setup option in your analysis cell (Static Structural in this case). This will

open the Ansys Mechanical window where we will define our boundary conditions and create

an analysis. Your components are available in Named Selections object.

Select the component on which you wish to apply a boundary condition. Right click and select

Insert to view the options. After selecting your choice, you can edit the parameters, like force

magnitude etc. in the details view. In the figures below, a Pressure of 100Pa is applied on a

region that we selected on the femur head, and a fixity boundary condition applied at the

bottom face.

If you have assigned materials in Mimics then an additional text file containing information

about materials is exported with the mesh. To load this file, first insert a commands object in

your outline as shown below.

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Next, right click on the Commands (APDL) object and select import. Select the text file

exported with your mesh from Mimics.

Now you have added the materials that were defined in Mimics.

Add solution visualization or post processing objects by right clicking on the solutions object

and selecting the analysis of your choice. Launch the solver by clicking on solve button in the

main menu.

After the solver has converged, you can analyze your results by clicking on your post

processing objects.


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11. Using Mimics with Simmetrix

11.1. Export a volumetric file from Mimics

We advise to use the Abaqus file format when linking between Mimics and Simmetrix. You

can export your volume mesh to an Abaqus file by going to the Export menu and choosing

Abaqus. This will show the following dialog:

Add the volume mesh you want to export to the list and click on the OK button.

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11.1.1. Export a surface mesh from Mimics

If you want to export your surface mesh to Simmetrix, export it as an ABAQUS file. To do this,

go to the Export menu and choose Abaqus.

You can export a 3D object from the list by selecting it, clicking on the Add button and then

clicking on the OK button.

11.2. Change the Abaqus pattern in Simmetrix

To make sure that you write out an Abaqus file in Simmetrix that can be imported in Mimics

you will have to change the default Abaqus pattern file in the Simmetrix software. This pattern

file will determine how an Abaqus file is written out exactly. To do this, first go to the

export/case/abaqus folder in the root directory of the SimAppS folder and make a backup of

the abaqus.sxp file in this folder.

After this open the abaqus.sxp file in a text editor (e.g. notepad) and change the contents of

the file to:

sxp 0

# abaqus.sxp created 28-Jan-2004 jat

# Write abaqus input file from input mesh

# Use mesh node ids

required = "mesh"

precision = 16

showpoint = 1

mfaceNormals = "off" # (runs faster when "off")

mregionIdOffset = 1


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# Create mesh nodes

mesh {

nodeMessage = function:makeNodes()

log:header = "$nodeMessage"

}

# Write first header

header = "*HEADING\n"

# Write mesh nodes

mesh/mnodes {

header = "*NODE\n"

item = "$id, $x, $y, $z"

}

# Set element-code based on mesh degree

map = "<1 'C3D4'> <2 'C3D10'>"

element-code = function:mapI2S($meshDegree,$map,"C3D???")

# Write element sets, 1 for each model region

# For now, only support linear tetrahedral

gmodel/gregions/* {

header = "*ELEMENT, elset=region$tag, type=$element-code\n"

mregions {

item = "$id, $(mnodes[*]/id)"

} # end context (mregions/*)

} # end context (gmodel/gregions/*)

# Remove mesh nodes

mesh {

nodeMessage = function:removeNodes()

log:header = "$nodeMessage"

}

11.3. Import Simmetrix files in Mimics

Now you can start Simmetrix, import the Abaqus surface mesh from Mimics and make a

volumetric mesh in Simmetrix. If you export this volumetric mesh to an Abaqus file you will be

able to import this file in Mimics to assign materials to it by going to the FEA/CFD menu and

choosing Import. This will open following dialog:

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Browse to the directory where you have saved the Abaqus volumetric mesh, select it and click

on the Open button. You can then start assigning materials to the volumetric mesh.

12. Using Mimics and Fluent To facilitate data exchange with Fluent, it is best to use the fluent mesh format. The .msh file

contains the triangle data from the STL file along with surface definitions. The notion of

surface definitions is important and therefore the msh file contains more information than the

STL file.

Especially for fluid flow simulation applications, surfaces are necessary to define inlet and

outlet of the flow. If only an STL is available, TGrid (Fluent‟s preprocessor) will read in the

STL and split the STL in surfaces according to a feature angle (comparable to our wireframe

angle). As the wireframe of STLs can be noisy, especially for scanned parts, we would end up

with many noise surfaces and unclosed wireframe and TGrid will not be able to recognize a

volume inside the surfaces.

This is where the Fluent mesh file proves its usefulness. In the fluent mesh file, we can write

correct surface definitions to make sure TGrid will recognize the volume.

12.1. Export the object to a Fluent file

When you have determined a good wireframe angle, you can go back to Mimics and export

the file by going to the Export menu and choose Fluent.



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When you click on OK, you can choose between using the current surface split or to resplit

using a defined angle.

12.2. Import the surface mesh in Fluent

You can then import this Fluent file in Fluent by using following parameters:

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12.3. Convert the surface mesh to a volume mesh

To convert your surface mesh to a volume mesh on TGrid (one of Fluent‟s preprocessors),

use the mesh controls indicated in the image below:

13. Empirical Expressions The tables below show some relationships between different density-, strength- and stiffness-

related parameters.

13.1. Expressions for Trabecular/Cancellous Bone

13.1.1. Expressions for the Femur – Distal

Apparent density R² Axis Young's modulus E (MPa) R² Sca Ref Tec

= 1.205 * HU + 139 0,77 A-P E = 0.01 * ^ 1.79 0,93 S1 R1 T1

= 1.205 * HU + 139 0,77 A-P E = 2.99 * - 423 0,84 S1 R1 T1

= 1.205 * HU + 139 0,77 M-L E = 0.01 * ^ 1.82 0,91 S1 R1 T1

= 1.205 * HU + 139 0,77 M-L E = 2.84 * - 416 0,85 S1 R1 T1

= 1.205 * HU + 139 0,77 S-I E = 0.82 * ^ 1.27 0,95 S1 R1 T1

= 1.205 * HU + 139 0,77 S-I E = 5.27 * - 384 0,91 S1 R1 T1

S-I E = 0.65 * ^ 1.31 - 48 0,92 S2 R2

13.1.2. Expressions for the Femur - Proximal


= 1.067 * HU + 131 0,84 A-P E = 0.004 * ^ 2.01 0,91 S1 R1 T1

= 1.067 * HU + 131 0,84 A-P E = 3.91* - 657 0,90 S1 R1 T1

= 1.067 * HU + 131 0,84 M-L E = 0.01 * ^ 1.86 0,89 S1 R1 T1

= 1.067 * HU + 131 0,84 M-L E = 3.64 * - 506 0,89 S1 R1 T1

= 1.067 * HU + 131 0,84 S-I E = 0.58 * ^ 1.30 0,94 S1 R1 T1

= 1.067 * HU + 131 0,84 S-I E = 4.56 * - 331 0,90 S1 R1 T1

S-I E = 1.02 * ^ 1.22 - 56 0,95 S2 R2

P E = 1.310 * ^ 1.4 0,91 S3 R3 T2

= 0.0019 * HU + 0.105 0,60 S4 R4

= 1 * HU P E = 0.0041 * ² + 2.1142 * + 54.75 0,57 S5 R5 T3

= 1 * HU P E = 0.0057 * ² + 3.0586 * + 178.42 0,47 S5 R5 T3


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13.1.3. Expressions for the Humerus - Proximal


= 0.624 * HU + 173 0,83 A-P E = 2.22 * - 169 0,88 S1 R1 T1

= 0.624 * HU + 173 0,83 A-P E = 0.06 * ^ 1.57 0,86 S1 R1 T1

= 0.624 * HU + 173 0,83 M-L E = 2.50 * - 201 0,86 S1 R1 T1

= 0.624 * HU + 173 0,83 M-L E = 0.07 * ^ 1.55 0,86 S1 R1 T1

= 0.624 * HU + 173 0,83 S-I E = 0.32 * ^ 1.41 0,92 S1 R1 T1

= 0.624 * HU + 173 0,83 S-I E = 4.25 * - 270 0,92 S1 R1 T1

S-I E = 5.11 * ^ 0.97 - 301 0,92 S2 R2

13.1.4. Expressions for the Major Metaphyseal Regions


= 1 * HU A E = 1.3665 * - 38.644 0,79 S6 R6 T4

= 1 * HU A-P E = 1.6201 * - 97.448 0,68 S6 R6 T4

= 1 * HU M-L E = 1.0976 * - 60.822 0,43 S6 R6 T4

= 1 * HU S-I E = 1.3988 * + 39.069 0,58 S6 R6 T4

= 0.001141 * HU + 0.11837 0,82 S6 R6 T4

13.1.5. Expressions for the Patella


Could not be measured A-P E = 0.005 * ^ 1.91 0,86 S1 R1 T1

Could not be measured A-P E = 3.37 * - 976 0,88 S1 R1 T1

Could not be measured M-L E = 0.0005 * ^ 2.21 0,91 S1 R1 T1

Could not be measured M-L E = 3.49 * - 1352 0,86 S1 R1 T1

Could not be measured S-I E = 0.04 * ^ 1.68 0,87 S1 R1 T1

Could not be measured S-I E = 5.65 * - 1327 0,85 S1 R1 T1

S-I E = 3.64 * ^ 0.99 -1002 0,88 S2 R2

13.1.6. Expressions for the Spine - Lumbar


= 1.122 * HU + 47 0,69 A-P E = 1.92 * - 170 0,92 S1 R1 T1

= 1.122 * HU + 47 0,69 A-P E = 0.02 * ^ 1.69 0,86 S1 R1 T1

= 1.122 * HU + 47 0,69 M-L E = 2.20 * - 209 0,94 S1 R1 T1

= 1.122 * HU + 47 0,69 M-L E = 0.02 * ^ 1.75 0,89 S1 R1 T1

= 1 * HU S-I E = 7.136 * - 172.3 0,73 S7 R7 T1

= 1.122 * HU + 47 0,69 S-I E = 5.82 * - 349 0,96 S1 R1 T1

= 1.122 * HU + 47 0,69 S-I E = 0.63 * ^ 1.35 0,94 S1 R1 T1

S-I E = 8.24 * ^ 0.95 - 489 0,96 S2 R2

13.1.7. Expressions for the Tibia - Proximal


= 0.916 * HU + 114 0,80 A-P E = 0.06 * ^ 1.51 0,89 S1 R1 T1

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= 0.916 * HU + 114 0,80 A-P E = 1.52 * - 98 0,86 S1 R1 T1

= 0.916 * HU + 114 0,80 M-L E = 0.06 * ^ 1.55 0,90 S1 R1 T1

= 0.916 * HU + 114 0,80 M-L E = 1.81 * - 124 0,88 S1 R1 T1

= 1 * HU S-I E = 82.3 * ^ 8.29 0,63 S8 R8 T5

= 1 * HU S-I E = 1.91 * + 33.2 0,61 S8 R9 T5

= 0.00130 * HU + 0.103 0,87 S-I E = 1371 * ^ 1.33 0,63 S8 R10 T5

= 0.00130 * HU + 0.103 0,87 S-I E = 1173 * - 44.38 0,55 S8 R11 T5

= 1 * HU S-I E = 2.11 * + 76.5 0,55 S8 R12 T6

= 1 * HU S-I E = 117 * ^ 7.36 0,54 S8 R13 T6

= 0.00130 * HU + 0.103 0,87 S-I E = 2132 * ^ 1.46 0,61 S8 R14 T6

= 0.00130 * HU + 0.103 0,87 S-I E = 1689 * - 99.4 0,57 S8 R15 T6

= 1 + 0.001 HU S-I E = 35.48134 * r ^ 11.7 0,61 S9 R9 T7

= 1 * HU S-I E = 80.6 * ^ 7.74 0,63 S10 R10 T5

= 1 * HU S-I E = 1.76 * + 30.4 0,61 S10 R10 T5

= 0.00120 * HU + 0.101 0,88 S-I E = 1371 * ^ 1.33 0,63 S10 R10 T5

= 0.00120 * HU + 0.101 0,88 S-I E = 1173 * - 44.38 0,55 S10 R10 T5

= 1 * HU S-I E = 1.94 * + 75.1 0,55 S10 R10 T6

= 1 * HU S-I E = 116 * ^ 6.85 0,54 S10 R10 T6

= 0.00120 * HU + 0.101 0,88 S-I E = 1689 * - 99.4 0,57 S10 R10 T6

= 0.00120 * HU + 0.101 0,88 S-I E = 2132 * ^ 1.46 0,61 S10 R10 T6

= 1 * HU S-I E = 78.3 * ^ 6.96 0,64 S11 R10 T5

= 1 * HU S-I E = 1.54 * + 25.0 0,61 S11 R10 T5

= 0.00106 * HU + 0.0949 0,89 S-I E = 1371 * ^ 1.33 0,63 S11 R10 T5

= 0.00106 * HU + 0.0949 0,89 S-I E = 1173 * - 44.38 0,55 S11 R10 T5

= 1 * HU S-I E = 1.74 * + 59.6 0,57 S11 R10 T6

= 1 * HU S-I E = 109 * ^ 6.33 0,56 S11 R10 T6

= 0.00106 * HU + 0.0949 0,89 S-I E = 1689 * - 99.4 0,57 S11 R10 T6

= 0.00106 * HU + 0.0949 0,89 S-I E = 2132 * ^ 1.46 0,61 S11 R10 T6

= 0.916 * HU + 114 0,80 S-I E = 5.54 * - 326 0,95 S1 R1 T1

= 0.916 * HU + 114 0,80 S-I E = 0.51 * ^ 1.37 0,96 S1 R1 T1

S-I E = 0.50 * ^ 1.38 - 20 0,96 S2 R2

13.2. Expressions for Cortical Bone

13.2.1. Expressions for the Mandible


S-I E = 0.024 * - 23.93 0,37 S14 R1 T8

R E = 0.013 * - 13.05 0,54 S14 R1 T8

13.2.2. Expressions for the Tibia


S-I E = 0.013 * - 3.842 0,53 S14 R1 T8

= 1 * HU B E = 0.00704 * 0,30 S15 R11 T9

= 1 * HU B E = 0.06456 * ^ 0.74 0,30 S15 R11 T9

13.2.3. Expressions for the Humerus



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S-I E = 0.015 * - 6.326 0,72 S14 R1 T8

C E = 0.011 * - 8.540 0,66 S14 R1 T8

R E = 0.011 * - 9.212 0,69 S14 R1 T8

13.2.4. Expressions for the Femur


S-I E = 0.014 * - 6.142 0,77 S14 R1 T8

C E = 0.009 * - 4.007 0,47 S14 R1 T8

R E = 0.010 * - 6.087 0,61 S14 R1 T8

13.3. Legend

13.3.1. Definitions

Apparent density = hydrated tissue weight / bulk volume

Effective density = (hydrated tissue + marrow weight) / bulk volume

13.3.2. Anatomical Axis (Axis)

A-P Anterior-Posterior

M-L Medial-Lateral

S-I Superior-Inferior

P parallel to neck axis

A Average

R Radial

B Bending

C Circumferential

13.3.3. Scanner Types (Sca)

S1 Phillips Tomoscan AV (120 kVp, 150 mAs)

S2 Ultrasonic Testing

S3 GE 8800 (120 kVp, 240mAs)

S4 GE 8800 (120 kVp)

S5 Philips Tomoscan AVE1 (120 kV, 100 mA, 1s)

S6 Technicare HPS 1440 (130 kVp, 100mA, 4s) / GE 9800

S7 Philips

S8 EMI 7070 (140 kVp & 40mA)

S9 EMI 7070 (140 kV, 70mA, 3s)

S10 EMI 7070 (120 kVp & 50 mA)

S11 EMI 7070 (100 kVp & 60 mA)

S12 Phillips Tomoscan AV (120 kVp)

S13 Siemens Somatom DR3

S14 Phillips Tomoscan AV (120 kVp, 150 mAs)

S15 GE 9800 CT (120 kVp, 140 mA, 3s)

13.3.4. Literature Reference (Ref)

R1 Rho, Hobatho, Ashman, 1995

R2 Rho, Hobatho, Ashman, 1997

R3 Lotz, Gerhart, Hayes, 1990

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R4 Esses, Lotz, Hayes, 1989

R5 Pattijn, 2004

R6 Ciarelli, Goldstein, Kuhn, Cody, Brown, 1991

R7 Rho, Zerwekh, Ashman, 1991

R8 Hvid, Bentzen, Linde, Mosekilde, Pongsoipetch, 1989

R9 Bentzen, Hvid, Jørgensen, 1987

R10 Hvid, Bentzen, Linde, Mosekilde, Pongsoipetch, 1989

R11 Snyder, Schneider, 1991

13.3.5. Technique used to determine Young’s modulus (Tec)

T1 Ultrasound velocity measurement at 50kHz

T2 Destructive compression test (15% strain)

T3 Destructive compression test at high strain rate

T4 Non-destructive/destructive compression test

T5 Destructive compression test

T6 Non-destructive compression test

T7 Compression test

T8 Ultrasound velocity measurement at 2.25 MHz

T9 Three point bending

13.4. References

Ciarelli, M.J., Goldstein, S.A., Kuhn, J.L., Cody, D.D., Brown, M.B. “Evaluation of Orthogonal

Mechanical Properties and Density of Human Trabecular Bone From the Major Metaphyseal Regions

with Materials Testing and Computed Tomography” Journal of Orthopaedic Research, Vol. 9, No. 5

(1991) 674-682

Esses, Steven I., Lotz, Jeffrey C., and Hayes, Wilson C. “Biomechanical Properties of the Proximal

Femur Determined In Vitro by Single-Energy Quantitative Computed Tomography” Journal of Bone and

Mineral Research, Vol. 4, No. 5 (1989) 715-722

Harp, John H., Aronson, James, and Hollis, Marcus. “Noninvasive Determination of Bone Stiffness for

Distraction Osteogenesis by Quantitative Computed Tomography Scans” Clinical Orthopaedics and

Related Research, No. 301 (1994) 42-48

Hobatho, Marie-Christine, Rho, Jac Y., Ashman, Richard B. “Anatomical Variation of Human Cancellous

Bone Mechanical Properties In Vitro” Studies in Health Technology and Informatics, Vol. 40 (1997) 157-

173

Hvid, Ivan, Bentzen, Soren M., Linde, Frank, Mosekilde, Lis, and Pongsoipetch, Buntoing. “X-Ray

Quantitative Computed Tomography: The Relations to Physical Properties of Proximal Tibial Trabecular

Bone Specimens” Journal of Biomechanics, Vol. 22, No. 8/9 (1989) 837-844

McBroom, R.J., Hayes, W.C., Edwards, W.T., Goldberg, R.P., White, A.A. “Prediction of Vertebral Body

Compressive Fracture using Quantitative Computed Tomography” Journal of Bone and Joint Surgery,

Vol. 67-A, No. 8 (1985) 1206-1214

Rho, J.Y., Hobatho, M.C., and Ashman, R.B. “Relations of Mechanical Properties to Density and CT

Numbers in Human Bone” Medical Engineering and Physics, Vol. 17, No. 5 (1995) 347-355

Taylor, W.R., Roland, E., Ploeg, H., Hertig, D., Klabunde, R., Warner, M.D., Hobatho, M.C.,

Rakotomanana, L., Clift, S.E. “Determination of Orthotropic Bone Elastic Constants Using FEA and

Modal Anslysis” Journal of Biomechanics, Vol. 35 (2002) 767-773


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CHAPTER 7: Simulation

The Mimics Simulation module allows you to simulate surgical procedures.

Overview of Simulation Functionality

Anthropometric Analysis

Simulation of surgical procedures

Validate design of implants

Planning osteotomies and/or distractions

Easy repositioning of bone slices both with and without the use of a distractor

Note: In order to be able to use distractors in the Simulation Module, you will have to install the distractor database. You can find this installation file on the Mimics CD or on our website at the Mimics download section.

1. Starting Simulation All Simulation functions are loaded immediately in Mimics after registration of the Simulation

module. When the module is registered, a few extra items are visible in the interface:

On the menu bar:

An extra CMF/Simulation menu, listing the different Simulation functions and Design

functions is added. The soft tissue simulation module is also listed here in case you also

have registered the simulation module.

In the Measurements menu and in the Measurements Toolbar, there's a

Draw/Manipulate Nerve button added.


Extra Simulation tab.

Extra buttons on the 3D Objects tab: select a 3D Object and click on the Move or Rotate

buttons to move or rotate the selected 3D Object.

Note: If you're not able to start the Simulation module, you probably haven't entered the passwords yet. Go to Options > Licenses and fill in the correct passwords.

2. Simulation tab

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List of created Objects


Visible Lists if the object is visible or not by means of glasses. You can change the

visibility by clicking on the glasses.

Contour Visible Lists if the contour of the objects visible on the 2D images or not by means of


glasses.

Diameter Shows the diameter of the Nerve.

Functions on Objects

New This will show the menu of the objects you can create. You can choose

between Cutting Path, Distractor, Mirror Plane and nerve.

Copy Copies the selected object to the clipboard. The object can then be pasted in

a 3-matic project or another Mimics project.

Note: Due to copyright policies, distractors cannot be copied.


Properties Displays the properties of the selected object:

In the properties dialog of a cutting path, you can change the name, color,

depth, thickness and the extensions at the front and the end of a cutting path.

You can also define if the cutting path should be closed or not.

The Preview button can be used to preview the adjusted cutting path before

applying the changes.

In the properties dialog of a distractor, you can change the name and color of

the distractor. You can also view some information about the distractor.


327

In the properties dialog of a mirror plane, you can change the thickness, width

and height of the mirror plane.

In the properties dialog of the nerve, you can change the name, color and

diameter of the nerve.

3. Simulation Menu When the Simulation module is licensed, the Simulation menu appears in the menu bar. This

menu lists different features of the Simulation module:

3.1. Measure and Analyse

To launch the Measure and Analyze tool, select the corresponding option from the

Simulation menu.


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3.1.1. Analysis Overview

When you click on the Overview button in the Anthropometric Analysis pane, the following

dialog will emerge.


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3.1.2. Creating a new template

To create a new template, simply click on „New‟ in the overview dialog. A window will pop up

allowing you to enter the desired analysis name in the „Analysis‟ field.

Points

When you click on the New button of the Points section, a second field in the pop-up window

allows you to define landmarks for the analysis. New landmarks can be created, copied,

edited or deleted. Each landmark can have some default properties that can be set when

creating the landmark or by editing an existing landmark using the „Edit‟ function. The

properties that can be set are the landmark name, its color and a description. The landmark

name can only be set at creation time. If you wish to import existing landmarks, refer to the

relevant section in this manual.

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Planes

By clicking on the New button in the Planes section, you can add planes to the template. To

define a plane you must first have defined points, or -alternatively- you can define a plane

based on other planes you have already created in the template.

Measurements

In the last field, measurements can be added to the template. Distances, angles and volumes

can be measured. For distance either the distance between two points or the distance

between a point and a plane can be measured. As for angle, this can be measured using 3

points or using 2 lines (defined by 2 points each). A volume can be measured by selecting at

least 4 points. A convex polygon will be created with those points and the volume will be

measured. Note that measurements can only be done using points or planes that have

already been defined in the template.


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3.1.3. Duplicating an existing template

If you wish to create a copy of an existing template, simply click in the „Active‟ column behind

the template you wish to duplicate. A green flag will appear.

Now click on „Copy‟ to create the copy. A new window will pop up allowing you to define the

template in a similar way as explained under creating a new template.

3.1.4. Editing an existing template

To change the properties of an existing template, activate the template by clicking in the

„Active‟ column behind the template. A green flag will appear. Click on „Change‟ and edit the

template as desired.

Note: You cannot change the default templates that are installed with the Simulation module. If you wish to edit the properties of one of the default templates you need to first create a copy of the template and then edit the copy.

3.1.5. Removing an existing template

If you wish to remove a template, activate it (the should appear behind the template name)

and then click on „Delete‟.

Note: You cannot delete any of the templates that are installed by default with the Simulation module.

3.1.6. Importing Points

Adding points from other templates

You do not need to define existing points again if you are creating a new template. Existing

points can be imported quite easily from other templates with the „Import‟ function. Simply

activate the template in which you wish to import the existing point(s) and click on the button

„Import Points‟. A new window will pop up.

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From the drop down menu choose the template where you want to import points from. All

points in that template are then shown in the window, select the point(s) you wish to import

and click on the „import‟ button. If points from other templates also need to be imported select

that template from the menu and repeat the steps above. To finish the import click on „ok‟.

Of course, since default templates cannot be changed it is not possible either to import points

into those templates.

3.1.7. Getting Started

The Anthropometric analysis tool allows for easy analysis and measurement based on pre-

defined templates in both 3D and 2D views. To start the Anthropometric Analysis, go to the

Simulation menu and choose Anthropometric Analysis.

Choosing the type of analysis

Before starting the analysis you first have to choose the analysis template you wish to use

from the Anthropometric analysis pull down menu.

If you do not find a template that coincides with your requirements you can create your own

template as described in the creating a new template section. When you have chosen the

template you wish to use, indicate the appropriate points, planes and/or measurements as

described in the following sections.

a. Points of analysis

The points of the analysis pane provide you with a list of available points in the currently

selected template. Points that have already been indicated on the images appear in black, the


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others appear in gray. The pane allows you to indicate, locate, edit or clear the points in the

list.

Indicating points

To place a point, first select it from the list and click on the „Indicate‟ button. You can indicate

a point in both the 2D and the 3D views. Note that you first need to indicate the point before

you can use any of the other option in the pane. When you have clicked the Indicate button,

the description of the point will be displayed.

You can always move the points of the analysis after their indication. If you are not able to

select the landmark points, first enable the right mouse mode by clicking on the Indicate

button. Now you will be able to move the points.

Locating points

If you want to easily view the image on the location where a point was placed, highlight the

point and click on „locate‟. This will move both the axial and the sagittal view to the position

where the point is located. Also a short description of the point you want to locate is given.

Clearing points

If you have misplaced a point you can easily remove it by selecting the point in the list and

clicking on the „clear‟ button.

Editing points

After having indicated a point you can change its properties. If you click on the „edit‟ button

you can easily change the color in which the point is shown on the images. You can also

change the position of the point here by changing its coordinates.

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b. Planes of analysis

The pane for the planes of analysis allows you to indicate and edit the planes defined in the

template.

Indicating planes

If you select the plane you want to view on the 3D image and click on „Indicate‟ a pop-up will

ask you to indicate the different points that define the plane. If these points were already

indicated the plane is shown automatically.

Editing planes

The „edit‟ option in the planes pane allows you to change the properties of the selected plane.

You can choose its thickness, change its color, width and height and select what opacity the

plane should have in the image.


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c. Anthropometric 3D measurements

If your current template includes measurements, a list of these measurements is provided in

the anthropometric measurements plane. These measurements can be easily indicated on

the images.

Indicating measurements

Select the measurement you wish to indicate and click on the „indicate‟ button. A window will

pop up to guide you through the placement of the points needed by the measurement. If

these points where already indicated on the images, the measurement will have been made

automatically.

Viewing/exporting/printing measurement details

It is also possible to display a more detailed view of the measurements. Click on „Details‟ and

a new window will appear showing all measurements with their pre-operative and post-

operative values for both 2D and 3D. These values can be easily referenced to a set of

normal; values that can be loaded with the „Load normal values‟ option. This overview can be

printed out or exported to a csv-file for easy importing in other programs.

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d. Sagittal plane

In case the CT images were not taken with the head of the patient at a 90-degree angle to the

table, 2D and 3D measurements will be off. Therefore it is possible to adjust the position of

the sagittal plane to account for this.

To change the position and direction of the sagittal plane, click on „Change‟ and draw the

plane in your axial view. To return the plane to its original position, use the „Reset‟ option.


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3.2. Cut

3.2.1. Cut Menu

There are three different cutting tools available: Cut with Polyplane, Cut with Curve and

Cut Orthogonal to Screen:

3.2.2. Cut with Polyplane

To launch the cut with polyplane tool, select the corresponding option from the Simulation Cut

menu.

The following window will appear and your cursor will change in a pencil.

With this pencil you can draw your cutting path in 3D or in 2D. After drawing, you can adjust

the properties of the cutting path by clicking on the Properties button.

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The cutting path will be visible in 3D and in 2D (if the option "Contour Visible" is selected)

Functions on Objects to Cut


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Show only selected

objects




Functions on Cutting Paths

New Allows you to create a new cutting path.

Properties Displays the properties of the selected cutting path:

In this properties dialog you can change the depth, thickness and the

extensions at the front and the end of the cutting path. You can also define if

the cutting path should be closed or not.

The Preview button can be used to preview the adjusted cutting path before

applying the changes.

Visible Lists if the cutting path is visible or not by means of glasses. Click on the

glasses to change the visibility of the cutting path.

Contour Visible Lists if the contour of the cutting path is visible or not by means of glasses.

Click on the glasses to change the visibility of the contour of the cutting path.

Cutting paths can be adjust after their creation by left-clicking on the points of the cutting path

and dragging them. You can also change the angle of the cutting path by left-clicking and

dragging the red arrow on the cutting path.

3.2.3. Cut with Curve

By defining a contour on the 3D object you can make more complex cuts.

To launch the cut with curve tool, select the corresponding option from the Simulation Cut

menu.

The following window will appear and your cursor will change in a pencil.

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Indicate points all around the 3D object to indicate your cutting path. When you indicate the

points, a red line will appear on the 3D that represents your cutting line. You finish the cutting

path by double clicking the left mouse button (or click once the right mouse button). A yellow

line will appear which represents the extension of the cutting path. This extension can be

adjusted in the main dialog box. Make sure that the extensions aren‟t crossing the 3D object.

The cut will only complete when all extensions are floating above the 3D object.

You can still adjust the control points. Select a point by holding the left mouse button and drag

to a new location.

After you‟ve checked the extensions click OK, the object is now cut AND split at the same

time.






Show only selected

objects




Functions on Cutting Lines

Indicate Shows the indicate tool and enables you to indicate a cutting line.

Close Closes the cutting line.

Delete Last Deletes the point of the cutting line that was drawn last.

Extensions Sets the distance between the cutting line and its extension

3.2.4. Cut Orthogonal to Screen


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To launch the cut orthogonal to screen tool, select the corresponding option from the

Simulation Cut menu.

The following window will appear and your cursor will change.

You have to select an object to cut from the list before you can preview or apply the cut.






Show only selected

objects




Functions on Cutting Lines

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Indicate Shows the indicate tool and enables you to indicate a cutting line.

Close Closes the cutting line.

Delete Last Deletes the point of the cutting line that was drawn last.

3.3. Split

To launch the split tool, select the corresponding option from the Simulation menu.

The following window will appear:

Functions on Objects to Split





Show only selected

objects


All parts

Largest part

Two largest parts

This way you can choose which parts you want to keep, all cut parts, only the

largest part or only the two largest parts.



To split, you always need a cut first (with the cutting tool)


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Then you select which object you want to cut and press the Preview and/or the Apply button.

3.4. Reposition

To launch the reposition tool, select the corresponding option from the Simulation menu.


3.4.1. Objects to reposition

First, select the object(s) you want to reposition.

Functions on Objects to Reposition





Show selected only Makes the selected objects visible and the unselected objects invisible.

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3.4.2. Translation and Rotation

Objects can be translated and/or rotated. For each type of manipulation the measure can be

adjusted to suit your needs.

3.4.3. Move with mouse

Objects can also be manipulated using the mouse. If the option „Move with Mouse‟ is enabled,

a box and arrows will appear around the object in both 3D and 2D views. If you grab the

center of the box -marked by a yellow rectangle- you can move the object around in all views.

By clicking on one of the arrows you can move the 3D object along an axis.

To rotate an object, select the „Rotate with Mouse‟ options. Rotation handles will be shown on

the 3D object. You can rotate the 3D object around the X, Y and Z axis by grabbing one of the

colored rotation handles. You can also rotate the 3D around the axis perpendicular to the

camera view by grabbing the outer ring of the rotation tool. To change the rotation center grab

and move the middle of the tool.

The values of translation and rotation are shown in the status bar.

3.4.4. Restrict DOF

Several restrictions on the manipulation of an object can be chosen. Possible restrictions are:

translating over axis, translating over plane, rotating over an axis and rotating over a point. Off

course unrestricted manipulation is also an option.

3.4.5. Registration

With the registration function, you can move landmark points that are located on the surface

of a 3D object and the 3D object will then automatically be moved according to the new

position of the landmark points. If you have not created any landmark points, you can do this

in the Anthropometric Analysis tool.

When you click on the Registration button, you will see a list of all the indicated landmark

points. Select the points you want to use from this list.


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When you click on the OK button, the following dialog will appear for each selected point:

In this dialog you can move each point by specifying a Lateral, Vertical and Rostral placement.

When you click on the OK button, the new position of the 3D object will be calculated and the

3D object will be moved to that position.

3.4.6. Switching/saving Positions

A few buttons are available in this step in order to facilitate the object manipulation. It is

possible to save a position and to afterwards easily return to that position. The home position

of the object can always be reached by clicking on „Go to Home Position‟.

3.4.7. Motion Analysis

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An analysis overview of the motion will be displayed if you click on the Analyze Motion

button.

3.4.8. Finishing the reposition

If the repositioning of the objects matches the situation you want to achieve, you can click

„Finish‟.

3.5. Place Distractor

To place a distractor, select the corresponding option from the Simulation menu.

You can place a distractor on an existing object or on a part of an object. For this, you first

need to cut and split.


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By selecting 'Place Distractor' from the Simulation menu the following window will appear:

Functions on Objects to place the distractor on






Select on which part you want to place your distractor and click Next. A distractor library will

appear in which you can chose which distractor you want to place.

After selecting the distractor from the library the following window will appear:

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Locate the distractor with two mouse clicks in the 3D view. The first click determines the point

of the distractor on the fixed part of the bone, the second mouse click determines the point of

the distractor on the moveable part of the bone.

3.5.1. Adjust the Distractor Position

The direction of the distraction vector can be adjusted with the following window. The

distractor can also be aligned to the sagittal or axial slices or to the Frankfurt plane.

You can also change the vector of the distractor by left-clicking on the red arrow originated

from the distractor and dragging the arrow.

3.6. Reposition with Distractor

To launch the reposition tool, select the corresponding option from the Simulation menu.

Functions on Objects to Reposition with the distractor







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3.6.1. Translating according to the Vector of the Distractor

After you have selected the object to be repositioned you will be able to use the „Translate

distractor‟ option. To translate the distractor simply use the „-‟ and „+‟ buttons. The default

translation for each step will be 1mm but this can be change by editing the field in between

the two translation buttons. Of course, it is not possible to move a distractor beyond its

starting or ending position, using a distraction measure that is too large will simply put the

distractor in its starting, resp. ending position. The total translation of the distractor is shown

underneath the translation buttons.

3.6.2. Switching/saving Positions

A few buttons are available in this step in order to facilitate the object translation. It is possible

to save a position and to afterwards easily return to that position. The home position of the

object can always be reached by clicking on „Go to Home Position‟.

3.6.3. Analyze Motion

An analysis overview of the motion will be displayed if you click on the „Analysis Overview‟

button. Note, however, that an analysis can only be made of you have first saved the position

you wish to analyze.

3.7. Soft tissue

After you simulated the maxillofacial surgery with the Simulation functions (osteotomy or

distraction), you can check how the soft tissue will change according to the new bone

positions.

The Soft tissue module also allows you to map a picture of the patient on top of the soft-tissue.

3.7.1. Soft-tissue simulation

To launch a new Soft tissue simulation, select the corresponding option from the Soft tissue

menu.

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The following window will pop up, and the 3D objects in the 3D window will disappear.

First select the postoperative hard tissue objects. The ones you select will also become

visible in the 3D window.

Note: For optimal results of the Soft tissue simulation, the spine should be included as hard tissue. If the spine is not segmented, you can go to the segment module (if you have SimPlant Pro) and segment in a very easy way the spine.

Then select the pre operative Soft tissue object. The selection will become visible in the 3D

window.


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Click Next and the Soft tissue simulation will start calculating. A progress bar on the bottom

shows you how long the calculation will take.

Note: The calculation time depends on the performance of your computer and the size of the data. It can range from a few seconds to a few minutes.

Once the calculation is completed, the Soft tissue simulation will appear on your screen. To

see the simulation, click the Play button. The speed of the animation can be adjusted by

using the Speed bar.

3.7.2. Photo Mapping

To launch a new Photo Mapping, select the corresponding option from the Soft tissue menu.


From the Object to photo map list select the pre-operative soft-tissue. Click on Load to

browse to the picture of the patient.

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Now indicate landmark points on the patient picture and indicate them on the 3D. Check the

preview checkbox to see how the photo mapped 3D model looks like. Click ok to see the 3D

model in the application.

3.8. Advanced tools

3.8.1. Merge

To launch the merge tool, select the corresponding option from the Simulation menu.


Functions on Objects to Merge


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Show only selected

objects




To merge, you always need to select two or more 3D objects or STLs. The selected objects

will then be merged to one STL by clicking on the Ok button.

3.8.2. Split

To launch the split tool, select the corresponding option from the Simulation menu.


Functions on Objects to Split





Show only selected

objects


All parts

Largest part

Two largest parts

This way you can choose which parts you want to keep, all cut parts, only the

largest part or only the two largest parts.



To split, you always need a cut first (with the cutting tool)

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Then you select which object you want to cut and press the Preview and or the Apply button.

3.8.3. Mirror

To launch the mirroring tool, select the corresponding option from the Simulation menu.



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Functions on Objects to Mirror





Show only selected

objects




Functions on Mirror planes

New Allows you to indicate a new plane. To do this, left-click three times in any 2D

or 3D view. A plane will then be constructed through those three points.

You can mirror a complete part of the bone, or a split part. This can be checked in 3D and in

2D.

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Select the part you want to mirror. Then select a mirror plane or create your own by clicking

on the New button and indicating three points of the plane in 2D or 3D.

With the Preview button you can check the result. If the result looks good, press Apply.


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3.8.4. Boolean

The boolean tool allows you to do a boolean operation (Minus, Unite or Intersect) between 3D

Objects, STLs or MedCAD Spheres and Cylinders. The result of the boolean operation will be

put in the 3D Objects list.

To launch the boolean tool, select the corresponding option from the Design menu.


Functions on Objects to Boolean





Show only selected

objects


Operation The boolean operation you want to perform on object 1 and 2.



3.8.5. Rescale

The rescale tool allows you to rescale 3D Objects or STLs. The result of the rescale operation

will be put in the 3D Objects list.

To launch the rescale tool, select the corresponding option from the Design menu.


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Functions on Objects to Rescale





Show only selected

objects


Factor You can choose the rescale factor in X, Y and Z direction.

Size The size field displays what the size of the object will be in X, Y and Z

direction with the specified factor.

You can also give in a size in X, Y or Z and the rescale factor will be

calculated automatically.

Uniform If the uniform option is selected, the rescale factor will be the same for X, Y

and Z direction.



4. Tools Menu The Tools menu is also activated when the Simulation module is licensed. This menu

includes two functions for modifying the surface of the 3D objects after the 3D calculation: the

Smoothing and the Triangle Reduction tools.

4.1. Smoothing

The smoothing tool allows you to smooth 3D Objects or STLs. The result of the smoothing

operation will be put in the 3D Objects list.

To launch the smoothing tool, select the corresponding option from the Design menu.



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Functions on Objects to Smooth





Show only selected

objects


Iterations You can choose how many smoothing iterations will be performed.

Smooth factor The smooth factor determines how much smoothing is performed.

Compensate shrinkage If the compensate shrinkage setting is enabled, the shrinkage of the object

due to the smoothing will be countered.



4.2. Triangle Reduction

The triangle reduction tool allows you to do a triangle reduction of 3D Objects or STLs. The

result of the triangle reduction operation will be put in the 3D Objects list.

To launch the triangle reduction tool, select the corresponding option from the Design menu.


Functions on Objects to Reduce Triangles





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Show only selected

objects


Reducing mode You can choose between a Point based triangle reduction, an Edge based

triangle reduction or an Advanced Edge based triangle reduction.

Tolerance The Tolerance indicates the maximum deviation in mm that a related triangle

may have, to be part of the same plane that contains the selected triangle.

Edge Angle The Edge Angle-value defines which angle should be used to determine

edges of the part that cannot be removed. Triangles deviating less than this

angle will be grouped into the plane of the other triangles.

Iterations You can choose how many triangle reduction iterations will be performed.

5. Nerves toolbox This tool allows you to create a representation of nerves. Note that this is only a

representation of the nerve channel as you have drawn it.

The nerve is drawn manually and consists of a series of points, connected by an interpolated

line. Select the nerve icon from the tools toolbar or select the Tools menu and then

Draw/manipulate nerve. The nerves toolbox will appear on the screen. Each time only the

relevant buttons are enabled in the toolbox. Close the toolbox by clicking on the black cross in

the top right corner or by clicking again on the nerve button in the tools toolbar.

5.1. Draw a nerve

This function allows you to draw the nerve. These are the steps to perform:

Select the Create nerve tool. The cursor will change to a pencil.

Start drawing the nerve: for every change in direction along the nerve, you need to click

(press and release the left mouse button) once to define the course of the nerve. In order

to terminate the nerve, double click the left mouse button or click the right mouse button.

While drawing the nerve you can scroll through the images with the cursor keys and

follow the nerve channel if needed.

Fine adjustments can be made by dragging the points to a new location. The nerve can

be moved entirely by dragging the orange line.

5.2. Select a nerve

Select the cursor tool and click on a nerve to select it. The points of a selected nerve are in

white. The points of a non-selected nerve have the same color as the lines of the nerve. The

action you do is always performed on the selected nerve.

5.3. Delete a nerve

Select the nerve you want to delete and click on the Delete nerve button.


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5.4. Add a point to a nerve

Click on the Add point to nerve button, hover the mouse over the nerve segment were you

want to add the point. The cursor will change into a pencil, click your left mouse button to add

a point.

5.5. Remove a point from a nerve

Click on the point of the nerve you want to delete. The selected point will be colored green.

Click on the Remove point from nerve button to delete the point.

5.6. Show the list of nerves

Click on this button to display the Nerves tab on the project management.

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PART V

Mimics Tutorial


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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

(http://www.materialise.com/materialise/view/en/2595102-Download.html). You will need to

register first or, if you are already registered, sign in using your e-mail 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 Tutorial that shows how you can import images in Mimics

Chapter 2: Mimi 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 Tutorial that shows how to use the MedCAD module.

Chapter 5: Obturator Tutorial that shows how to make a mold of a cavity by segmenting the

Soft tissue around the cavity.

Chapter 6: Manual Import Tutorial that shows how to use the manual import function.

Chapter 7: FEA Tutorial 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 Tutorial that shows how to use the FEA module for linking to CFD.

Chapter 10: Non-manifold

Assemblies

Tutorial that shows how to combine two meshes.

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.


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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 New Project Wizard. In the File

Browser window, you can select where the images to be imported can be found (STEP 1).

Browse to the MedData folder and select the folder called “Import1” in the File browser. The

list of files will be displayed in the Filename column and all the files will be automatically

selected. Click on one of the files and press CTRL+A to select all files in that folder. Click the

Next button.

An Import log window will show details of the import, including the recognized formats of the

file (see the general help files for a list of known formats).

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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).

Click Next to proceed to the Studies page. This is the second step of the New 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. You can also compress your

studies to cut off unwanted regions like Air. For this case, we will chose Lossless

Compression.


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Now you may click the Convert button and you will see a progress bar. After the images are

successfully imported, youwill see a Check Orientation window where you can check and

change the orientations of the imported study. Here, the orientation strings L and R stand for

Left and Right, A and P stand for Anterior and Posterior, and T and B stand for Top and

Bottom respectively. To change the orientation, click on one of the letters and chose the

correct orientation from the list. Note that all the other orientation strings are updated

automatically.

If some orientation is not defined in the DICOMs, you will see an X mark, indicating a missing

orientation. You can click on the X mark and assign an orientation to it.

If the orientation of the images is correct, click OK and your Mimics project will open. 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.

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First of all you can get a better look at the images by 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.

You may 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).

3. Semi-automatic import Now we will try to import the Bitmap images you can find in your MedData directory in the

"Import2" subdirectory. elect File > New Project Wizard and browse to the

C:\MedData\Import2\ directory. Click on one of the images in Import2 folder and press

CTRL+A on your keyboard to select all files in it. Press the Next button and the Import Log

will be displayed. Click Next to see the Images Properties dialog.


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Here you can preview your images and order them according to your preferences. You can

also check if the scan resolution is correctly read. Uncheck force isotropic sampling checkbox

and change the Z direction to 1. You can also change the dimensions of your images. This

information will be typically provided by the radiologist who took the scan. Correct values

should be entered here to ensure correct dimensions of the volumes and the 3D objects that

will be created further on. Leave it in mm scale for this case and click Next.

In the Edit Images dialog, you have the option to crop the images or resample them. For this

example, we will leave the values as is and click Next.

Now you should be able to set the orientation parameters as described in the previous

paragraph and calculate a good 3D.


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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.

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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).

In the Mimics window, you will see several indicators, intersection lines, tick marks etc. To

deactivate an indicator, go to View > Indicators in the Menu Toolbar, and toggle them off.

In the right border of the window you will see a slider that allows you to scroll through the

images from the active view.

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


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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:

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 straight-line

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.

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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.

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.


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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 .

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.

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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 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.

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.


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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.

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Click the Next button to proceed; the Calculation Parameters dialog box is displayed. Fill in

the values as displayed below.


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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.

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When one contour file is selected, the Next button in the “RP slice – Mask/3dd/contour file

selection” window opens the window displayed below.


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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 50.00 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!!

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9. View of end result


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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

Windowing

Thresholding

Region growing

Editing

Artifacts

Multiple particles

Scan prosthesis

Boolean Operations


1. Opening the project In the File menu, select Open (Ctrl+O). Double click the Simon.mcs file.

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

-30.50). 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.

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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

2.4.1. 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.


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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.

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 -4.50. 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.

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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 64.50 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.

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.


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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 87.25 (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 -4.50 and -3.50 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.

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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.

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.


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Sagittal image after local thresholding

2.4.2. Artifacts

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.

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

2.4.3. Multiple particles

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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 “Yes”.

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.

2.4.4. 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


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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!

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

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.

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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. 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.



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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


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 CAD-systems 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).


2.1. 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.

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 Growing 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 2.

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3. 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 Calculate 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.

3D view of the polylines

You can also calculate polylines by clicking the button in the segmentation toolbar.

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.


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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 -511. Afterwards, 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

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.

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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: -483 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.

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.


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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:

Objects fitted on the Polyline sets Imported STL files

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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.


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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


Windowing

Orientation

Thresholding

Editing

Region growing


1. Case study

1.1. 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.

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.

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The implant, called an obturator prosthesis, was cast from the mold in a bio-compatible

silicone.

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.


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2.1. Preparation of the data

In the File menu, select Open (ctrl+O) or click the button . Double click the obturator.mcs

project.

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.

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 and draw a line in the axial image over the

cavity.

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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.


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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.

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.

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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).

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.

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


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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.

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.

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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.

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 the figure below. You can also enable transparency using the

button.


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CHAPTER 6: Import Raw images 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:

Raw Import

Edit images

1. Raw import

1.1. Import images

Select New Project Wizard from the File menu. In the New Project Wizard select all the

images at "MedData\Import3" directory and click Next.

If the images are in Raw format, the New Project Wizard will automatically take you to the

following steps. You can also force raw import by checking the Force raw import checkbox

at the bottom right of the dialog. If this option is checked, Mimics will import all images as

RAW images. When you press the Next button, you will see that the files are recognized as

“unknown files” in the “Import log” window. Click Next to go to the Raw image properties

window.

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In the Raw image properties window you will have to enter the parameters of the scan,

namely, the Scan resolution, the Image parameters and the Pixel properties. This information

is usually provided along with the scan by the radiologist. For this case, the Scan resolution is

0.5 X 0.5 X 1 mm and the Image parameters are 256 X 256 pixels. The pixel values are in

Signed Short format with Low byte order Byte swapping. When you have entered the correct

parameters, you can preview the images and Next button will be activated.

Following is some more explaination on the parameters.

1.1.1. Scan resolution

Here the sizes of the pixels have to be entered. For this example, each pixel are 0.5mm in X-

direction, 0.5mm in Y-direction and 1mm in Z-direction. If the image slices are taken axially,

then Z-direction would be equivalent to slice distance.

1.1.2. Image parameters

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.


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The number of pixels in vertical and horizontal section is the height and the width of the

images. Common sizes of images are: 256 * 256, 512 * 512 and 1024 * 1024. In this example,

the images have a resolution of 256*256.

1.1.3. Pixel properties

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

If you fill these values in, you will see that Mimics will set the file header size to 8432 bytes.

Byte swapping determines the order in which the images are read. You can try different

options for byte swapping parameter and preview the images. For this case, when High byte

first is chose, there are local distortions all over the image, because the data is read in the

wrong order.

For this example, the pixel type is Signed Short and Low Byte First for the parameter Byte

Swapping.

1.1.4. Study information

Here you may fill in an appropriate name for the patient name. This will be the name that is

used for your project.

2. Edit images If the images look good in the preview, click the Next button in the Raw image properties

window. In the Edit images window, you may crop or resample the images.

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Click on the Pixel Mapping tab to view the histogram of the pixels. Here you can also map the

pixel grayvalues to a custom range by moving the sliders from the ends of the histogram. For

this case, the imported pixel grayvalues will be mapped to a 16 bit grayvalye range, as shown

here.

Click Next and the you will see the familiar Check orientation window, where you can set the

orientation into the Mimics project.


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CHAPTER 7: Simulation

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.


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).

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.

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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:

Click the Region Growing 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.


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5. Calculating a 3D

Go to the Project Management by clicking its icon and choose the Masks tab.

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.

Click on the Calculate 3D button.

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The Calculate 3D 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.

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.


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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:

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.

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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:

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:


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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.

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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

Simulation menu and choose Measure and Analyse.


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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.

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.

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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 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 fine-tuning 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.


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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.

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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.


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CHAPTER 8: FEA

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.


Opening the Project

Calculating a 3D

Remeshing the 3D

Creating the volume mesh based on the remeshed 3D

Material Assignment

Exporting the Volumetric Mesh


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.

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/CFD menu and choose Remesh. You will notice that there are

two 3D models, select the Yellow 1 3D model. The FemurShaft model will be used in the non-

manifold assembly tutorial.

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3-matic will open with the part already loaded for remeshing. Select the part and click on the

button Create Inspection Scene to inspect the quality of the mesh.

There are several Shape parameters available to measure the quality of the triangles. For this

example we will use the Height/Base(N) 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.


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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 0.4. 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 15.124 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 32.168.

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

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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

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: If 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 Laplacian (1st 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.

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.


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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.

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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.

STEP F: Call the self-intersection test. Go to Fixing -> Mark self-intersecting 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.


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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 .

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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 0.4. 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 0.1.


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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.

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.

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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:

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.


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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 = -13.4 + 1017 * 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 = -388.8 + 5925 * Density.

STEP E: Check the values for the materials that will be assigned in the material editor:

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STEP F: 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:


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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.


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CHAPTER 9: CFD

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.


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 New Project Wizard. Browse to the directory where you have

installed the extra Tutorial Files and go to the Airway directory. Follow the steps to import a

DICOM file as in Chapter 1.

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.

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 92.70/55.20.

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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.

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 icon.

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:


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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:

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Make sure your interface is looking like the screenshot below:

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.


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Perform the same procedure on the outlet. Press the Esc key to unselect the mark tool.

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.

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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 parameters section. In the Histogram parameters 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.


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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:

Then Apply the Auto-Remesh operation again with following settings:

This will result in following 3D Object and quality histogram:

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As you can see, there are no more triangles with a quality below 0.4.

4.4. 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:


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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.

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Select again the Smoothing function , make sure the Marked triangles are selected and

click on apply.

Click on the Unmark button in the mark toolbar again to unmark all triangles.

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:


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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:

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.

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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:


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CHAPTER 10: Non-Manifold Assembly

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.


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


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.

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

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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.

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.


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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.

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 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:

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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.


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Click on OK, to finish the cut.

The cut will create a new 3D model, PolyplanCut-Yellow. To split this model, go the

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.

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:

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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.

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 non-manifold 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


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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 function . Select the

non_manifold_assembly and click on Apply.

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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.


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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 -> 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: 0.1, iterations 5, enable preserve surface contours.

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5.6. Auto remesh

In the next step we will optimize the triangle shape. In this tutorial we will use the

Height/Base(N) shape measurement. Select the Height/Base (N) measure from the Shape

measure dropdown box.

In the histogram drag the upper slider to 0.3, this is the quality needed in order to generate a

volume mesh.

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.


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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.

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.

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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.

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.


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Check Clip ON and adjust the position of your section.

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:

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PART VI

Extra Information


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CHAPTER 1: System Requirements Mimics runs under Windows 2000 and XP. It operates on any Pentium class personal

computer as long as the video memory is at least 4MB so that it supports a 1024x768

resolution with 24 bit colors. The monitor should be a high quality, non-interlaced color

monitor to ensure sharp and accurate images. We recommend a fast 3D video card that

supports DirectX to speed up the complex 3D calculations used by Mimics.

If you intend to purchase a computer for Mimics, we strongly urge you to use the

Recommended Specifications as a guide. If you are installing Mimics on an existing computer

system, please refer to the Minimal Specifications to ensure that Mimics will operate on your

computer.

Minimal Requirements:

Software:

Windows 2000 Service Pack 3, XP

Internet Explorer 5.0

Hardware:

Intel Pentium III - 500 MHz or equivalent

256 MB RAM

Graphics card supporting 1024x768 and 16-bit color with 4 MB RAM

Non-interlaced 15" color monitor

Recommended:

Software:

Windows XP, Vista or 7 (x64 edition is needed for Mimics 64-bit)

Directx 9.0

Internet Explorer 6.0

Hardware:

Intel Core 2 Duo / AMD X2 AM2 or equivalent

2GB RAM

5GB free hard disk space

Resolution of 1280x1024 or higher

Graphics card supporting 256 MB RAM

Optical mouse with a scroll wheel


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CHAPTER 2: Frequently Asked Questions

Import module 1. Mimics does not recognize the MOD device.

The drivers are installed together with the Mimics software. Our drivers operate with the OD

and they take care of reading and converting of the data. In order to do this, the drive has to

be connected correctly. It's also important that the user has administrator rights, in order to

access the SCSI devices. The following questions help to detect the problem:

When you start the PC, do you see the drive displayed in the list? This is important to know

whether the PC recognizes the drive. If this is not the case, the drive is not correctly

connected. A bad wire, a terminator problem, the dipswitch settings, or the SCSI address (0,1

or 7) can be the causes for this problem.

Are there other devices connected to the PC, like a tape drive, a ZIP drive? If yes, try without

any of these other drives connected.

If the SCSI device is listed during start-up, start Mimics and choose "Advanced SCSI" in the

Options menu. Start testing the SCSI devices. If you don't see the drive in the list, see our

troubleshooting page in the help files (via General, CT-Convert, Trouble Shooting).

2. Each time I select Import images from the File menu, my computer reboots.

When importing images, Mimics tries to contact the connected SCSI devices. The reason why

it causes problems is that one (or more) of these devices give error messages. In mimics

there is a function to block the messages from certain devices, so that this problem doesn't

occur anymore. Open Mimics and select from the file menu: Options --> Advanced SCSI. In

the dialog box that appears, disable the Enable SCSI checkbox. Click OK, restart Mimics and

try to import again.

3. When I convert Tiff images I got no-contrast images, even though the preview

window looked good.

In the Manual import dialog you see at the right bottom corner "Maximum Image Value". If this

value is a lower than the real maximum value in the dataset, it may cause images without

contrast, once they are converted.

4. When I import images and use CT compression, I get no-contrast images in Mimics.

When using lossless compression, the images look fine.

CT compression is a lossy compression. When you select CT compression during conversion,

the first 200 gray values in the data set will be changed to the Hounsfield unit -1024. This CT

compression is useful in datasets with a wider range of gray shades, where it will filter out the

noise in the air. Mimics also provide a lossless compression.

If you have a dataset with a narrow gray value range, most of these gray values will be put on

-1024 HU and this may cause images without contrast.

5. When trying to import DICOM images, the message "Cannot process DICOMDIR" is

shown and nothing is read.

It's probably a DOS formatted disk with DICOM images that is being read. On these disks

there's normally a file called DICOMDIR that lists all the images on disk. If this file can't be

found, then Mimics can't import the images and gives you this warning. Check if the disk is

not empty, because it's very strange for the DICOMDIR to be missing...

6. Are data sets with varying slice distances supported?

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If the file format is supported, the images are automatically read and converted. The table

position is read from the header of the file and used afterwards in the Mimics, so varying

distances are supported. You can simply read the table position on the axial view in Mimics.

When a manual import is needed (because the file format is not known), the situation is a bit

more complicated but not impossible. You will need to know all parameters upfront, so also

which image is on which table position. This info should be stored in a txt file that has to load

via the "Import table positions from" function in the Manual conversion window. When you

know this, you can create a dataset based on these images.

If there are groups of images with the same size (= sets of succeeding images), each of these

sets can be imported, set per set. But you have to make sure that you adjust the "first table

position" parameter for every set. Like this, you can pile up all images again at the correct

position.

7. How to read images from Unix formatted disks?

Unix formatted disks can be read like other optical disks in Mimics 7.2 and later versions. The

images need to be uncompressed. A TAC Helicoidal Marconi Twin is an example of a

scanner that writes UNIX formatted disks.

8. Input of Mimics

The Raw data is the data as it comes off the scanner in Fourier space. It is unreconstructed.

The reconstructed images slices are input for Mimics, not the volume data/RAW data without

header. Mimics can read all images that are parallel, have the same size and contain gray

values. If the images are binary, it's no problem for Mimics to read them, but it will not be

possible to generate a nice 3D model. If the scanner and/or file format is unknown, it can be

implemented/supported if we get the help of the customer. Since the scan site is customer, it

is easier for them to obtain the information about disk formatting and file formatting from the

scanner manufacturer. Having this information makes it easier for us to implement this.

9. When I import images from an MOD, my patient is not listed.

First check both sides of the optical disk. If it's a Picker MOD, then you must know that only 1

data block can be read from this MOD. This means that only 1 patient can be read at a time.

In order to read all patient data, they have to put each patient data on a different Picker MOD.

STL+ 10. When I export an STL file, I can’t find the file in the target folder.

Make sure you have the permission to write to the target folder. It could be that only users

with administrator rights have the permission to write to certain folders. Also check if the

option "hide file extensions for known types" is unchecked in Windows Explorer > View Menu

> Folder Options. Make also sure that there is enough space on the hard disk.

11. The size of the STL file becomes so high that it's very difficult to handle in

LightYear software.

You should use the direct interface: in the RP Slice module you can calculate SLC files that

can be loaded in the Lightyear software. This method has 3 advantages:

1. No problem with big file sizes, because it is already sliced.

2. Cubical interpolation can be applied. The model will look less stair-stepped.

3. High resolution can be kept.

Once the SLC file is loaded in Lightyear, you just have to click "prepare". Also calculate the

support file with RP Slice!


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General 12. I had a few times a blue screen while working with Mimics.

Typically such errors are caused by a defect memory or a corrupt disk, in other words,

hardware problems.

13. How to organize images.

Open the project in Mimics and go to File --> Organize images. All images with a V-sign will

be used in the project. To leave out some of the images you can proceed in two ways:

1) In the list on the left, you can select all images you want to leave out the project and then

click on the V-sign of a line. Or you can use the Add and Remove buttons on the bottom of

the window. All selected images will be left out of the project.

2) Click on an image in the preview window on the right to leave it out of the project. If you

want it back into the project, click again on the image.

14. If a patient is rescanned, then written to the same optical disk as the previous scan,

how can you tell which is the old scan and which is the new scan?

You can't tell from the import images dialog box what scan is the old one or the new scan.

The projects are not listed in a chronological order. In the Open project dialog box, you can't

find it out either. The only way to distinguish between them in this situation is to convert them

both, open them one by one in Mimics and look in the project information dialog box to see

the study date and time (if this is available in the header file).

15. What are the deviations between the dimensions of a reconstructed model of a

reference or calibration body compared to its real dimensions?

Because our interpolation algorithms are designed to be able to use sub pixel values, the 3D

reconstruction calculation has a maximal error of 1/2 pixel size (mostly at max. 0.2 mm).


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CHAPTER 3: ITK Disclaimer

Copyright (c) 1999-2003 Insight Software Consortium

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted

provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of

conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of

conditions and the following disclaimer in the documentation and/or other materials

provided with the distribution.

Neither the name of the Insight Software Consortium nor the names of its contributors

may be used to endorse or promote products derived from this software without specific

prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED

TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A

PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


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CHAPTER 4: Contact Info

Website:

http://www.materialise.com/mimics

Europe (Headquarters) Materialise

Technologielaan 15

3001 Leuven

Phone +32 16 39 66 11

[email protected]

USA & Canada Materialise

3009 Miller Road

Ann Arbor, MI 48103

Phone +1 734 662 5057

[email protected]

United Kingdom AMP Technology Centre

Advanced Manufacturing Park

Brunel Way, Catcliffe

Sheffield, S60 5WG

Phone +44 1142 541 248

[email protected]

Germany Argelsrieder Feld 10

D- 82234 Oberpfaffenhofen

Phone +49 8153 88 12 -0

[email protected]

France Zone Industrielle

41, Avenue de la Déportation

26100 Romans-sur-Isère

Phone +33 4 75 05 00 22

[email protected]

Ukraine Ul. Raisy Okipnoi 8a

02002 Kiev

Phone +380 44 594 56 10

[email protected]

China Room 1803A , BaoAn Mansion

No. 800 Dongfang Road, Pudong

Shanghai, PRC 200122

Phone + 8621 58312406

[email protected]

Japan Materialise Japan K.K

Yokohama Portside Bldg. 2F

Sakae-cho 8-1

Kanagawa-ku, Yokohama

Phone +81 45 440 4591

[email protected]

Malaysia Materialise

Unit 906&907, Block A, Phileo Damansara 2

No 15 Jln. 16/11

46350 Petaling Jaya

Selangor

Phone +60 3 76652988

[email protected]

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