Mimics 14 Reference Guide

Mimics 14.
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Reference Guide v14.1.2/ July 2011
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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
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 MRIscans. 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.
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.
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
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.
STEP 3:
After reading the license agreement, select the I accept the terms of the License Agreement checkbox and click on the Next button.
STEP 4:
Select your region and click Next.
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.
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STEP 6:
Select if you want to install the Demo Files or not and click on Next.
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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.
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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.
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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.
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STEP 10:
The Mimics software gets installed. This can take a few moments. This window will close automatically when the progress bar is finished.
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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. Its recommended to reboot your computer to finalize the installation.
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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.
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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
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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:
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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:
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Browse to the location where the key file is stored. When youve 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.
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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.
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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.
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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:
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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.
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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:
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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:
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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.
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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
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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.
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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.
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PART II General Information
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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 Axial Sagittal Coronal 3D view Parallel Cross-sectional
Color Red Green Orange Light-green Yellow (these images are only visible after performing an online reslice) 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
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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: Lossless Compression CT Compressed MR Compressed Air Compressed Lossy JPEG Compressed Lossy JPEG & CT Compressed Lossy JPEG & MR Compressed Lossy JPEG & Air Compressed Case: No compression was used while importing JPEG compression was not used during saving CT compression was used while importing JPEG compression was not used during saving MR compression was used while importing JPEG compression was not used during saving Cut Air compression was used while importing JPEG compression was not used during saving No compression was used while importing project was saved with JPEG compression CT compression was used while importing project was saved with JPEG compression MR compression was used while importing project was saved with JPEG compression Cut Air compression was used while importing project was saved with JPEG compression
and and and and and and and 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.
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4.1. Toggle transparency

You can show the 3D object opaque or transparent. Click on the button to toggle between opaque and transparent view. in the 3D toolbar
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 clipping can be changed in the clipping tab: . The settings of the
Active
By default one axial clipping plane is active. To make more planes active, make sure to check the active icon .
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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 a clipping direction or to unlock. to lock
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:
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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.
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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 belong to the different views: Red Axial Orange Coronal Green Sagittal . The reference planes take over the colors that
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Cross Sectional Parallel
Blue 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
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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
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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.
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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 crosssectional 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 Cross-section Parallel Sagittal Coronal Red Blue (only visible if the project is resliced in Reslice Layout) Yellow (only visible if the project is resliced in Reslice Layout) Green 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 Axial Sagittal Coronal Numbering Increasing from bottom to top Increasing from the right to the left side of the patient 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 rightclick on an image, on the 3D view, on a 3D object, a STL, a CAD object, ...
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There are several easy shortcuts available from the default context menu:
Pan View Zoom Unzoom Zoom to full screen 3D Window Enables the panning mode Enables the zoom mode Unzooms the view Zooms the view to full screen Enables the 3D view in the window
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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: right-drag with your mouse button 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
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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.
Zoom to full screen on axial view
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.
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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 leftclicking 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 Visible Lower Threshold Higher Threshold Name of the mask. By clicking on the name of the mask, it can be renamed. Lists if the mask is visible or not by means of glasses. Lower Threshold setting of the mask. 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. Deletes the selected mask Gives numerical information of the selected mask Duplicates the selected mask Clears the contents of the selected mask, the threshold of the mask is kept Opens the Calculate 3D window Lists the available function on the selected mask
Delete Properties Duplicate Clear Calculate 3D Action
1.1.3. Properties
The mask properties give numerical information about the gray values in the selected mask:
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Threshold low Threshold high Minimum value Maximum value Average value Standard deviation
Lower threshold value used for the 3D objects calculation Higher threshold value used for the 3D objects calculation Minimum gray value in the selected mask Maximum gray value in the selected mask Average gray value from the selected mask
Number of pixels Mask volume Scale
Amount of pixels in the selected mask The volume of the mask 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 Visible Contour Visible Name of the 3D, by clicking on the name of the 3D, it can be renamed. Lists if the 3D is visible or not by means of glasses. 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. 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. 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 which was set before calculation, possible options are: low, medium, high, optimal, custom.
Triangles Visible
Transparency
Quality
1.2.2. Functions on 3D reconstructions

New Copy Delete Properties Duplicate Move Rotate Action Creates a new 3D. The Calculate 3D window appears. Copies the 3D to the clipboard. The 3D can then be pasted in another project. Deletes a 3D object. Gives the properties of the calculated 3D object. Duplicates the selected 3D model. Activates the handles to move the STL to a new positions Activates the handles to rotate the STL around its axis 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. Lists if the polyline is visible or not by means of glasses. Tells on which mask the polylines were calculated. If the set is grown out of another set, it is independent of a mask.
Visible Based On
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1.3.2. Functions on Polyline sets

New Copy Delete Duplicate Color Polyline growing Creates a new polyline set. The Calculate Polylines window appears. Copies the polyline set to the clipboard. Deletes a polyline set Duplicates the selected polyline set Changes the color of a polyline set The polyline Growing tool provides the capacity to create several sets of polylines. Lists the available functions on the select polyline set
Action
1.4. STLs
1.4.1. List of created Objects

Name Visible Contour Visible Name of the object. By clicking on the name of the object, it can be changed. Lists if the object is visible or not by means of glasses. 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. 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. 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.
Triangles Visible
Transparency
1.4.2. Functions on Objects

Load Copy Loads an STL file into the project. Copies the STLto the clipboard. The STL can then be pasted in a different project. Removes an STL file from the project. Displays the properties of the selected STL file.
Remove Properties
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Mimics 14.1 Reference Guide Duplicate Export STL Move Duplicates the selected STL file. Saves the selected STL file (with its current position). When the Move button is enabled, you can move the STL in the 2D views and the 3D view. When the Rotate button is enabled, you can rotate the STL in the 2D views and the 3D view. Lists the available functions you can perform on the selected STL Opens the transformation dialog:
Rotate
Action Transform
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 of the measurement. Lists if the measure is visible or not by means of glasses. 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). Indicates the units corresponding to each measurement value.
Name Visible Value
Unit
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Deviation Area
The deviation in Hounsfield units or grey values for a density measure. The area in mm 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. Deletes one or more measures. Shows the properties of the selected measurement. Duplicates the selected measurement. Updates all views to show to selected measure. Only angle and distance measures can be located. Lists the available function on the selected measurements
Delete Properties Duplicate Locate
Action
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 Visible Cross-Section Length (mm) 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. The active reslice object is indicated by means of glasses. In the Reslice layout the images corresponding the active reslice object will be shown. 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 Delete Properties Duplicate Shows a menu from where you can choose to reslice along a curve or along a plane. Deletes one or more reslice objects. Shows the properties of the selected reslice object. Duplicates the selected reslice object.
1.7. Annotation
1.7.1. List of the created Annotation

Name Visible Object Text Name of the annotation. The name is generated automatically based on the object on which the annotation is attached The visibility of the annotations is set by means of the sunglasses Lists the object to which the annotation is attached 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 Duplicate Locate Action
Opens the Annotation Properties dialog Duplicates the selected annotation Updates all views to show to selected annotation. 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 CTRL + Z CTRL + Y CTRL + F CTRL + I CTRL + SHIFT + M Open the Online Help Undo last action Redo last action Enable/Disable the Navigation Toolbar Makes all mask invisible 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. Exit Mimics 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
Alt + F4 SPACE
Shortcuts on files
CTRL + O CTRL + P CTRL + S CTRL + N Open a file Print a file Save a file Close a file
Shortcuts on the views

ArrowUp ArrowDown PageUp PageDown CTRL + L Right mouse button Go to next slice Go to previous slice Go 10 slices up Go 10 slices down Make slice indicators visible/invisible 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 Pan: Move the mouse while keeping the buttons pressed to pan. button CTRL + Right mouse Zoom: Move the mouse vertically while keeping the buttons pressed to zoom
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button Backspace
in and out. Toggles between zoomed in and unzoom.
Shortcuts on the 3D view

Arrow keys Page Up Page Down Home End SHIFT + keys above Scroll wheel ALT + left/right Rotate the 3D view left/right and up/down Rotate the 3D view 10 degrees down Rotate the 3D view 10 degrees up Rotate the 3D view 10 degrees left Rotate the 3D view 10 degrees right Pan the 3D view With the scroll wheel you can zoom in on the 3D view. Do washing machine rotation
Shortcuts on the layouts

F2 F3 F4 F5 Image Layout 3D Layout Reslice Layout Simulation Layout (if the simulation module is licensed)
Shortcuts on Segmentation functions

Region Growing
CTRL + R Start the Region growing function
Edit
CTRL + E While in edit mode: D E T ALT CTRL + drag left mouse button SHIFT + Left mouse button Open the edit toolbar and go in edit mode Draw Erase Draw with local threshold Holding the ALT key switches between Draw and Erase Resize the edit cursor Temporarily release the edit-tool and do 1-click navigation.
Shortcuts on text fields in dialogs

CTRL + C CTRL + X CTRL + V Copy Cut Paste
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Shortcuts on Movie Tool

CTRL + SHIFT+ M SHIFT+ F8 SHIFT+ F9 Start the movie tool Start Recording / Stop Recording 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: patients 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 -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 Patient Study ID Study Date File Displays the browse tree Displays the patient name Shows the study ID Shows the study date Displays the file name
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2.2. Functions
Add directory to Favorites Make default Delete folder Browse Adds the current Makes the selected folder your default To delete the selected folder from the list of favorites. 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. To delete the selected study from your computer. in Shows all the projects in the folder and subfolders Switches between the two browse modes. Quickly sort the studies by a column by clicking on the column header Change the order of the columns by dragging the column header to the left or the right Click on the Open button after selecting a study or double-click on a study to open it Closes the Open dialog box Opens the help pages on the Open project subject
Delete study Search Subfolders Switch view Sort by column Change order Open Cancel Help column
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 Remove
To change the name of the folder 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 STLs 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 STLs in the tree or in the list on the right and click the Load button, the selected STLs 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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Mimics 14.1 Reference Guide 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. 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. Unselected When marked all unselected images will be removed from the project. This action cannot be undone. 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.
Contrast
Delete images
Add/Remove
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 TopBottom 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 parallel view, click on this button: . , next to the parallel view. To return to the
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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 White background Dithering Resolution of the images Option to print a white background 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 Current page Range Print all pages Print only the page in the print preview 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 Edit Info Print Setup Page Setup Print To set some advanced print options. To add comments on the prints. To select the printer To define the page margins and the font. You can also choose the unit: mm or inch. 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 Objects to print Distances between images
Axial image
Select the pages to print. Select the objects to print. 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. 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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Mimics 14.1 Reference Guide 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 oneclick-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 Hide Volume Rendering Show Masks Hide Masks Show Measurements Hide Measurements Show Polylines Hide Polylines Show Annotations Hide annotations
make volume rendered 3D objects visible when they are invisible make volume rendered 3D objects invisible when they are visible make all masks visible when they are invisible make all masks invisible when they are visible make all measurements visible when they are invisible make all measurements invisible when they are visible make all polylines visible when they are invisible make all polylines invisible when they are visible make all annotations visible when they are invisible 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: right-drag with your mouse button 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
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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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Toggle 3D
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 patients 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.
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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 Hide Measurements...
Delete the measurement Hide the measurement 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 (mm), 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 Hide Measurements List...
Delete the rectangle Hide the rectangle 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 (mm), 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 Hide Measurements List...
Delete the ellipse Hide the ellipse 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 Text Rotation Text alignment Text
Style of the line ending Direction of the text Alignment of the test 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 Hide Properties Annotation List
Deletes the text annotation Hides the text annotation Opens annotation properties dialog 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 Visible Profile name of the profile line. Click on its name to change it (similar as in Windows Explorer). 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 Color Delete End / Start Thresholding Updates the 2D view to show the position of the profile line. Allows you to change the color of the selected profile lines. Deletes the selected profile lines. 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 Grid X-axis Grid Y-axis Allows you to see the vertical axis with all Hounsfield values or only the values lower than the maximum value along the profile line. To show or hide the vertical grid lines. 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 nonoptimal 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 isocontours 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 Delete Move Up / Down Help
Creates a new filter. Deletes a filter. Reorganizes the order of the filters. 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

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 dont 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. | -i | < d with 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 Multiple Layer Seed point Deviation
This feature enables filling internal gaps of the selected mask and places this in a new mask or in an existing one. 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. Shows the Hounsfield/Grayvalue of the last selected seed point. 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 (0255), 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 rightclicking 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 Automatic contour
The mask that will be created when applying the 3D LiveWire tool 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/ 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. 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. When you click on the Segment button, a mask is calculated based on the automatic contour.
Attraction
Apply parameters to range
Segment
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 Operation The Source mask is the mask that will be altered. 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. The new mask that will be created. 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. is the amount of pixels you will take/add in one operation
Target Limited to :
Number of pixels 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. 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. Draws in the active mask Erases in the active mask. To erase a full slice right-click in a view and select erase full slice from the context menu. 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
Tolerance/Impatience
Draw Erase
Threshold
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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 dont 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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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. Adds to the temporary mask. To select a full slice right-click in the slice and select select full slice. Deselects from the temporary mask. 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. 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.
Select
Deselect Copy to slices
Number of slices
Operation active mask
on
the 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. 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. Adds the indicated region to your selection Removes the indicated region from your selection The grow tool only selects the 3D model on which you applied the tool, discarding all loose parts. Inverts the current selection. Hides the current selection Showed the hidden selection Removes the current selection from the mask Moves the selection into a new mask
Width/Height
Select Deselect Grow
Invert Hide Show Removes Separate
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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. Dont 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 Z resolution Decides how many voxels are grouped in the XY plane 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 Mask Font
Enter label text here The mask that will contain this label 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 Depth Text size in mm 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. Determines if the label is 2D slice-able or not. 2D slice-able labels are restricted to horizontal or vertical direction. Orientation of label
2D slice-able label
Horizontal or Vertical
View from top or View Orientation of label from Bottom
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

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 Visible Contour Visible Name of the object. Lists if the object is visible or not by means of glasses. 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. 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.
Move
1.2. List of Landmark points

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

Name Visible Contour Visible Name of the object. Lists if the object is visible or not by means of glasses. Lists if the contour of the object is visible on the 2D slices or not by means of
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Mimics 14.1 Reference Guide 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.
2.2. List of Fixed Part

Name Visible Contour Visible Name of the object. Lists if the object is visible or not by means of glasses. 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.
2.3. Settings
Name Distance method Name of the object. threshold 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. 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. This number defines how many times the algorithm will be applied 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.
Distance threshold
Number of iterations Subsample percentage
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

Name Visible Contour Visible Name of the object. Lists if the object is visible or not by means of glasses. 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. 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.
Move
3.2. List of Masks

Name Visible Lower Threshold Higher Threshold Name of the object. Lists if the object is visible or not by means of glasses. Lower Threshold setting of the mask. 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 dont 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 Subtract Multiply Divide Difference GVr = GV1 + GV2 If GVr is higher than 4095GV, it is set to 4095. GVr = GV1 - GV2 If GVr is lower than 0GV, it is set to 0. GVr = GV1 x GV2 If GVr is higher than 4095GV, it is set to 4095. GVr = GV1 / GV2 GV1 is divided by GV2. GVr = Abs(GV1 - GV2)
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Average Min Max AND OR XOR Transparent
Opaque
The absolute value is taken of the difference between GV1 and GV2. GVr = (GV1 + GV2) / 2 The average is taken of GV1 and GV2. GVr = Minimum(GV1,GV2) The minimum is taken of GV1 and GV2. GVr = Maximum(GV1,GV2) The maximum is taken of GV1 and GV2. GVr = GV1 AND GV2 A bit wise AND is done of GV1 and GV2. GVr = GV1 OR GV2 A bit wise OR is done of GV1 and GV2. GVr = GV1 XOR GV2 A bit wise XOR is done of GV1 and GV2. GVr = GV1 x (GV2 / 4095) The grayvalue of Dataset 2 is determining the transparency of the voxels of Dataset 1. 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

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", "Axial521.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 Images Range Filename Path This area displays the masks that are currently available in your project. Select here the desired mask to process. You can choose for which view you want to export the mask area. 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. The name of the generated text file 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 Output directory This area displays the masks that are currently available in your project. Select here the desired mask to process. 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. You can change the file name of your Grayvalues file. At this time the only possible output format is txt (text file). Choose between Hounsfield units and Grayvalues.
File name Save as type Expressed in
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 Start from MedCAD Start Measure and Analyze Output directory This area displays the measurements that are currently available in the project. Shows the different CAD primitives available in the project Shows the Measure and Analyze point and reference planes available in the project 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 the text file to be placed. 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.
Objects to convert
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. In the options menu you can choose some general options and some options for the movie itself:
Options
View to capture Output Directory File Name
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. You can choose to capture the whole application, or only one of the views. When you click the browse button you select the location where you want your movie file to be placed. 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 Visualization 3D Masks Predefined Thresholds Import Annotation Printing Reslicing SCSI General settings like undo settings, autosave settings,... Settings about visualization of the indicators, view,... Settings concerning the 3D: the type of rendering, the 3D reference planes, performance settings,... Settings about colors and names of masks Settings about the Predefined Thresholds of the threshold toolbar Settings about preferences for the import wizard Settings about the font and background of the annotations Settings about the pages and objects to print. 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. 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. 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. Allows you to choose between a GreyValues scale or a Hounsfield scale.
STL Library Working Directory
Pixel Unit
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Mimics 14.1 Reference Guide HIPAA Hide Filename Hide Patient Name
Select this option to hide all file names, in the open project window, the project information window, ... 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
Maximum Undo Disk Space Autosave Settings
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. Indicates the maximum disk space that will be used to store information for the undo and redo operations. 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. When selected Mimics will use less memory for the visualization of the images.
Image
3-matic Preset
Path
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. 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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Mimics 14.1 Reference Guide 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 dont have a graphical card with hardware acceleration, select OpenGL or Direct3D (Use hardware not selected) or Software rendering. Visualization and navigation Defines the background color of the 3D view. To change this color click on 3D background color the colored square. Enhances the 3D visualization. This setting cannot be selected if you chose Use Gouraud shading Software rendering. This setting chooses the rotation axis of your 3D object. When the setting is Use world axis rotation enabled, the rotation will always be done around an axis perpendicular to the axial images. Performance Frees the memory when the 3D is not shown. Unload 3D from memory when invisible Use this option for faster loading of projects. All 3D objects will be set Hide all 3D when invisible when you open a project when this option is enabled. opening a project Will switch the 3D to a simplified representation when the frame rate drops Faster 3D interaction 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 Name Edit Mask in 3D ROI size Hide 3D objects Region of interest All 3D objects will be put on invisible when you select to edit the mask in 3D. 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. Allows you to change the color of the selected mask. Allows to change the name tag of the selected mask
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Restore Restores all mask preferences to its default settings.
3.5. Predefined Thresholds
List of Predefined Thresholds Name Lower Threshold Name of the predefined threshold Indicates the Lower Threshold in the pixel unit, selected in General preferences. Indicates the Higher Threshold in pixel unit, selected in General preferences.
Higher Threshold
Edit Predefined Threshold settings Edit Allows you to change the name, the Higher and Lower Threshold value of the
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Mimics 14.1 Reference Guide selected predefined threshold. Add Delete Reset Move Up Move Down Allows you to add a new predefined threshold Deletes the selected predefined threshold Resets the values of the predefined threshold to their original settings. Moves the predefined threshold up in the list. 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 Default color Opaque Images Nerves in Diameter defined as default for the creation of the nerve. Color defined as default for the creation of the nerve. 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. Allows you to choose the background color of the annotation box.
Box Background color
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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 Distance between parallels Maximum movement range
Spacing between two cross-sections. Spacing between two parallel images 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. The thickness used to calculate the parallel X-ray. If you don't select this setting you are able to navigate to virtually every
X-ray depth Snap to fixed positions
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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:
Opens the help page about the Toggle 3D button.
Opens the help page about licenses.
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.
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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 doesnt 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 dont know what module you need, import some images and Mimics will display the required module.
The provided modules are:

Siemens import GE Advantage import GE DAT import Philips import GE YMS import Dicom import Toshiba import Picker import Elscint import module for Siemens scanners module for General electric scanners module for General electric scanners, DAT medium module for Philips and Hitachi scanners module for Yokogawa Medical Systems scanners module for DICOM format module for the IS&C format of Toshiba scanners module for Picker format 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 theres 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 dont 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 displayed:
. The following parameter window is
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 youve 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 workstations 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. Its 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. If you have a .3dd file you wish to process, press this button in order to go to the RP Slice file selection window. 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. 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 support files to be placed.
Start from 3DD file
Start from contour file
Output directory
Masks/3dd/contour files 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 to convert 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. This table position indicates up to where the part should be made. Standard the highest position will be displayed.
Position Last Slice
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. Same as in X but in the Y direction. 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. Same as in X, but in the Y direction.
Y hatching distance X color hatching space
Y color hatching space
2.3.2. Build parameters
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Mimics 14.1 Reference Guide 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. 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 327 mm 535 mm 819 mm
Slice Resolution
200 100 80
0.005 mm 0.01 mm 0.0125 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). This parameter allows you to rescale the original object with a factor larger than 0.1 and smaller than 100.
Scale factor
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 Y Hatching Space The distance between two support walls in the x-direction. 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 Angle (2) in the drawing below. The length of the straight part: distance (3) expressed in numbers of layers. When this is checked, the perforation will also continue on the borders of the support.
Perforation Angle Nr. of straight layers Perforated Borders
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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 of the support structure (see picture). Be aware that the support will not go below 0 (in the z-direction). 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+).
Starting Height
Ending Height
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. This area displays the 3D objects that are currently available in your project. Select here the desired 3D object(s) to process. If you have a .3dd file you wish to process, press this button in order to go to the STL+ file selection window. This area displays the CAD objects that are currently available in your project. Select here the desired CAD object(s) to process. This area displays the FEA meshes that are currently available in your project. Select here the desired FEA mesh(es) to process. 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
Start from 3D
Start from 3dd File
Start from CAD
Start from FEA
Output directory
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Mimics 14.1 Reference Guide 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. 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. You can scale your object by changing the value in the edit field.
Objects to convert
Scale factor
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 scans), 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. Dont 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. 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. Makes the selected objects visible and the unselected objects invisible. Show selected objects Iterations Smooth factor Compensate shrinkage only
Contour visible
You can choose how many smoothing iterations will be performed. The smooth factor determines how much smoothing is performed. If the compensate shrinkage setting is enabled, the shrinkage of the object due to the smoothing will be countered. 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.
Keep originals
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. The following window will pop up:
Functions on Objects to Reduce Triangles

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. 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. 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. 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.
Contour visible
Tolerance
Edge Angle
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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

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects Smallest Detail Closing Distance Protect thin walls Corresponds to the size of the triangles on the newly created surface. Determines the size of gaps that will be wrapped away via the operation. 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. 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.
Contour visible
Keep originals
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:
Porosity Void Volume Total Volume
Average Pore diameter
Defined as the average of the diameters of the largest nonoverlapping spheres that can fit in the pores
Pore Size 1 n Pore size n i
Pore interconnectivity
Defined as the fraction of the void volume connected to the outside of the object, relative to the total void volume.
Pore Interconnectivity Void Volume connected to the outside Total void volume Surface area Total volume
Specific surface area Chamber pore size distribution Throat pore size distribution
Specific Surface Area
Describes, for each voxel, the largest overlapping spherical pore. 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.
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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 Visible Name of the object. By clicking on the name of the object, it can be renamed. Lists if the object is visible or not by means of glasses.
2.2. Functions on Objects

New Creates a new Object. The object menu appears :
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Mimics 14.1 Reference Guide Click on the desired object to go to the correct help page. Delete Properties Locate Action Deletes the selected objects. Displays the properties of the selected object. Locates the selected MedCAD object 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 Output directory This area displays the 3D objects that are currently available in your project. Select here the desired object to process. 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 Point Cloud file to be placed. You can change the file name of your Point Cloud file. At this time the only possible output format is ASCII.
File name Save as type
5. MedCAD Menu
5.1. MedCAD Menu
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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 To The set from where the polylines are grown The set to where the polylines are grown to. This can be an existing selection or a new created one. A measure for the strength of matching (%). This is done with a geometrical comparison. 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. 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.
Correlation
Auto multi-select
Keep Originals
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 Hide CAD Objects List
Deletes the selected point. Hides the selected point. 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. Click on the colored button in order to change the color of the MedCAD object.
5.4.4. Context menu
Deletes the selected line. Hides the selected line. 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). Click on the colored button in order to change the color of the MedCAD object.
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5.5.4. Context menu
Delete Hide
Deletes the selected circle. 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. Click on the colored button in order to change the color of the MedCAD object.
5.6.4. Context menu
Deletes the selected sphere. Hides the selected sphere. Opens the Objects tab page in the Project Management.
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. Click on the colored button in order to change the color of the MedCAD object. 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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Deletes the selected plane. Hides the selected plane. Opens the Objects tab page in the Project Management.
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.
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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. Click on the colored button in order to change the color of the MedCAD object.
5.8.4. Context menu
Delete Hide
Deletes the selected cylinder. 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 Set Check
Select the desired polyline set. This area (under the Polyline Set selection) indicates if the polyline set is valid for freeform curve generation. 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.
Order
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 on the screen. and the spline toolbox will appear
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 Set Check
Select the desired polyline set. This area (under the Polyline Set selection) indicates if the polyline set is valid for surface generation. 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.
Order
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 U en V parameters The surface can be closed or not. A parametric surface typically has 2 parameters: a u-parameter and a vparameter. 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 Number of iterations Distance control points
Select the minimum detail you want to resolve. Sets the amount of iterations you want the algorithm to perform.
between Sets the distance between two successive control points
5.11.1. Centerline properties
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Label Name Visualization Centerline color Highlight color Show branching points Branches Name Length(mm) Visibility Group The name of the branch Length of the branch The visibility of a branch can be toggled by clicking on the sunglasses. 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. Select a branch and click on delete to remove the branch from the list. You can export the centerlines as Iges files or export the coordinates of the centerlines and the measurements on the centerlines as Text file. Sets the color of the centerline. Sets the color of the highlighted branches of the centerline. Sets the visibility of the branching points on or off. Name of the centerline.
Delete Export
Export of centerline Properties
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Export Output Directory File Name Save as type Select the destination folder. Select the file name 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. Diameter of the inscribing circle in a control point. The measurement is exported as Dmin.
Minimal diameter
Maximal diameter
Diameter of the subscribing circle in a control point. The measurement is exported as Dmax. 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 midpoint. 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 in each control point. The Hydraulic diameter is exported
Curvature
Hydraulic Diameter
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as Dh. Hydraulic Ratio Circumference Hydraulic ratio in a control point. The Hydraulic ratio is exported as Xh. Perimeter of the surface in a control point. The measurement is exported as Scf. Area of the sectional surface normal to the centerline. The measurement is exported as Area.
Sectional 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. Diameter of the inscribing circle in a control point. The measurement is exported as Dmin. Diameter of the subscribing circle in a control point. The measurement is exported as Dmax. 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. 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) Hydraulic diameter in each control point. The hydraulic diameter is exported as Dh. Hydraulic diameter = (surface X-section) / (circumference X-section) Hydraulic ration in a control point. The hydraulic ratio is exported as Xh. Hydraulic ratio = (hydraulic diameter) / (subscribing diameter of Xsection) Perimeter of the surface in a control point. The measurement is exported as Scf. Area of the sectional surface normal to the centerline. The measurement is exported as Area.
Centerline Minimal Diameter
Centerline Maximal Diameter
Centerline Curvature
Centerline Tortuosity
Centerline Hydraulic Diameter
Centerline Hydraulic Ratio
Circumference
Sectional 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.
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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.
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2. FEA Mesh tab
2.1. List of created Objects

Name Visible Name of the object. By clicking on the name of the object, it can be renamed. Lists if the object is visible or not by means of glasses. You can change the visibility by clicking on the glasses. 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. 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.
Material
Contour Visible
2.2. Functions on Objects

Import Imports a volumetric mesh. For more information about the import process, please refer to the Import help page. Copies the selected volume mesh to the clipboard. The volume mesh can then be pasted into a 3-matic project or another Mimics project. Deletes the selected objects. Displays the properties of the selected object:
Copy
Delete Properties
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Duplicate Remesh
Duplicates the selected FEA mesh 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. Calls the window to do a material assignment for the selected object. Exports the selected object to a Patran neutral, Ansys, Abaqus or Fluent file.
Material Export
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.
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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
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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:
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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 doesnt 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 youve 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 reduce the number of triangles using a large angle value. to
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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 edge length (A). .Select from the inspection measure dropdown box Smallest
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 youve 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 subvolumes 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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Mimics 14.1 Reference Guide <Units>Hounsfield</Units> </Header> <Table> <Interval><Start> 0.0e0 <Interval><Start> 3.0e2 <Interval><Start> 6.0e2 </Table> </LookupTable>
</Start><Density> </Start><Density> </Start><Density>
0.0e0 3.0e2 6.0e2
</Density></Interval> </Density></Interval> </Density></Interval>
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 management tab: in the FEA project
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.
This will open following dialog:
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 project management tab: in the FEA
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 following interface:
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 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.
9.3. 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. Its 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 elements in our future releases.
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 following interface:
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 youre 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" mregionIdOffset = 1
# (runs faster when "off")
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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 (Fluents 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. This will open following dialog:
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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 Fluents preprocessors), use the mesh controls indicated in the image below:
13. Empirical Expressions

The tables below show some relationships between different density-, strength- and stiffnessrelated parameters.
13.1. Expressions for Trabecular/Cancellous Bone

13.1.1. Expressions for the Femur Distal
Apparent density = 1.205 * HU + 139 = 1.205 * HU + 139 = 1.205 * HU + 139 = 1.205 * HU + 139 = 1.205 * HU + 139 = 1.205 * HU + 139 R Axis Young's modulus E (MPa) R Sca Ref Tec 0,77 A-P E = 0.01 * ^ 1.79 0,77 A-P E = 2.99 * - 423 0,77 M-L E = 0.01 * ^ 1.82 0,77 M-L E = 2.84 * - 416 0,77 S-I 0,77 S-I S-I E = 0.82 * ^ 1.27 E = 5.27 * - 384 E = 0.65 * ^ 1.31 - 48 0,93 S1 R1 T1 0,84 S1 R1 T1 0,91 S1 R1 T1 0,85 S1 R1 T1 0,95 S1 R1 T1 0,91 S1 R1 T1 0,92 S2 R2
13.1.2. Expressions for the Femur - Proximal

Apparent density = 1.067 * HU + 131 = 1.067 * HU + 131 = 1.067 * HU + 131 = 1.067 * HU + 131 = 1.067 * HU + 131 = 1.067 * HU + 131 = 0.0019 * HU + 0.105 = 1 * HU = 1 * HU 0,60 P P E = 0.0041 * + 2.1142 * + 54.75 E = 0.0057 * + 3.0586 * + 178.42 R Axis Young's modulus E (MPa) R Sca Ref Tec 0,84 A-P E = 0.004 * ^ 2.01 0,84 A-P E = 3.91* - 657 0,84 M-L E = 0.01 * ^ 1.86 0,84 M-L E = 3.64 * - 506 0,84 S-I 0,84 S-I S-I P E = 0.58 * ^ 1.30 E = 4.56 * - 331 E = 1.02 * ^ 1.22 - 56 E = 1.310 * ^ 1.4 0,91 S1 R1 T1 0,90 S1 R1 T1 0,89 S1 R1 T1 0,89 S1 R1 T1 0,94 S1 R1 T1 0,90 S1 R1 T1 0,95 S2 R2 0,91 S3 R3 T2 S4 R4 0,57 S5 R5 T3 0,47 S5 R5 T3
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13.1.3. Expressions for the Humerus - Proximal

Apparent density = 0.624 * HU + 173 = 0.624 * HU + 173 = 0.624 * HU + 173 = 0.624 * HU + 173 = 0.624 * HU + 173 = 0.624 * HU + 173 R Axis Young's modulus E (MPa) R Sca Ref Tec 0,83 A-P E = 2.22 * - 169 0,83 A-P E = 0.06 * ^ 1.57 0,83 M-L E = 2.50 * - 201 0,83 M-L E = 0.07 * ^ 1.55 0,83 S-I 0,83 S-I S-I E = 0.32 * ^ 1.41 E = 4.25 * - 270 E = 5.11 * ^ 0.97 - 301 0,88 S1 R1 T1 0,86 S1 R1 T1 0,86 S1 R1 T1 0,86 S1 R1 T1 0,92 S1 R1 T1 0,92 S1 R1 T1 0,92 S2 R2
13.1.4. Expressions for the Major Metaphyseal Regions

Apparent density = 1 * HU = 1 * HU = 1 * HU = 1 * HU = 0.001141 * HU + 0.11837 0,82 R Axis Young's modulus E (MPa) A E = 1.3665 * - 38.644 A-P E = 1.6201 * - 97.448 M-L E = 1.0976 * - 60.822 S-I E = 1.3988 * + 39.069 R Sca Ref Tec 0,79 S6 R6 T4 0,68 S6 R6 T4 0,43 S6 R6 T4 0,58 S6 R6 T4 S6 R6 T4
13.1.5. Expressions for the Patella

Apparent density Could not be measured Could not be measured Could not be measured Could not be measured Could not be measured Could not be measured R Axis Young's modulus E (MPa) A-P A-P M-L M-L S-I S-I S-I E = 0.005 * ^ 1.91 E = 3.37 * - 976 E = 0.0005 * ^ 2.21 E = 3.49 * - 1352 E = 0.04 * ^ 1.68 E = 5.65 * - 1327 E = 3.64 * ^ 0.99 -1002 R Sca Ref Tec R1 R1 R1 R1 R1 R1 R2 T1 T1 T1 T1 T1 T1 0,86 S1 0,88 S1 0,91 S1 0,86 S1 0,87 S1 0,85 S1 0,88 S2
13.1.6. Expressions for the Spine - Lumbar

Apparent density = 1.122 * HU + 47 = 1.122 * HU + 47 = 1.122 * HU + 47 = 1.122 * HU + 47 = 1 * HU = 1.122 * HU + 47 = 1.122 * HU + 47 R Axis Young's modulus E (MPa) R Sca Ref Tec 0,69 A-P E = 1.92 * - 170 0,69 A-P E = 0.02 * ^ 1.69 0,69 M-L E = 2.20 * - 209 0,69 M-L E = 0.02 * ^ 1.75 S-I 0,69 S-I 0,69 S-I S-I E = 7.136 * - 172.3 E = 5.82 * - 349 E = 0.63 * ^ 1.35 E = 8.24 * ^ 0.95 - 489 0,92 S1 R1 T1 0,86 S1 R1 T1 0,94 S1 R1 T1 0,89 S1 R1 T1 0,73 S7 R7 T1 0,96 S1 R1 T1 0,94 S1 R1 T1 0,96 S2 R2
13.1.7. Expressions for the Tibia - Proximal

Apparent density = 0.916 * HU + 114 R Axis Young's modulus E (MPa) R Sca Ref Tec 0,80 A-P E = 0.06 * ^ 1.51 0,89 S1 R1 T1
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= 0.916 * HU + 114 = 0.916 * HU + 114 = 0.916 * HU + 114 = 1 * HU = 1 * HU = 0.00130 * HU + 0.103 = 0.00130 * HU + 0.103 = 1 * HU = 1 * HU = 0.00130 * HU + 0.103 = 0.00130 * HU + 0.103 = 1 + 0.001 HU = 1 * HU = 1 * HU = 0.00120 * HU + 0.101 = 0.00120 * HU + 0.101 = 1 * HU = 1 * HU = 0.00120 * HU + 0.101 = 0.00120 * HU + 0.101 = 1 * HU = 1 * HU = 0.00106 * HU + 0.0949 = 0.00106 * HU + 0.0949 = 1 * HU = 1 * HU = 0.00106 * HU + 0.0949 = 0.00106 * HU + 0.0949 = 0.916 * HU + 114 = 0.916 * HU + 114
0,80 A-P E = 1.52 * - 98 0,80 M-L E = 0.06 * ^ 1.55 0,80 M-L E = 1.81 * - 124 S-I S-I 0,87 S-I 0,87 S-I S-I S-I 0,87 S-I 0,87 S-I S-I S-I S-I 0,88 S-I 0,88 S-I S-I S-I 0,88 S-I 0,88 S-I S-I S-I 0,89 S-I 0,89 S-I S-I S-I 0,89 S-I 0,89 S-I 0,80 S-I 0,80 S-I S-I E = 82.3 * ^ 8.29 E = 1.91 * + 33.2 E = 1371 * ^ 1.33 E = 1173 * - 44.38 E = 2.11 * + 76.5 E = 117 * ^ 7.36 E = 2132 * ^ 1.46 E = 1689 * - 99.4 E = 35.48134 * r ^ 11.7 E = 80.6 * ^ 7.74 E = 1.76 * + 30.4 E = 1371 * ^ 1.33 E = 1173 * - 44.38 E = 1.94 * + 75.1 E = 116 * ^ 6.85 E = 1689 * - 99.4 E = 2132 * ^ 1.46 E = 78.3 * ^ 6.96 E = 1.54 * + 25.0 E = 1371 * ^ 1.33 E = 1173 * - 44.38 E = 1.74 * + 59.6 E = 109 * ^ 6.33 E = 1689 * - 99.4 E = 2132 * ^ 1.46 E = 5.54 * - 326 E = 0.51 * ^ 1.37 E = 0.50 * ^ 1.38 - 20
0,86 S1 R1 T1 0,90 S1 R1 T1 0,88 S1 R1 T1 0,63 S8 R8 T5 0,61 S8 R9 T5 0,63 S8 R10 T5 0,55 S8 R11 T5 0,55 S8 R12 T6 0,54 S8 R13 T6 0,61 S8 R14 T6 0,57 S8 R15 T6 0,61 S9 R9 T7 0,63 S10 R10 T5 0,61 S10 R10 T5 0,63 S10 R10 T5 0,55 S10 R10 T5 0,55 S10 R10 T6 0,54 S10 R10 T6 0,57 S10 R10 T6 0,61 S10 R10 T6 0,64 S11 R10 T5 0,61 S11 R10 T5 0,63 S11 R10 T5 0,55 S11 R10 T5 0,57 S11 R10 T6 0,56 S11 R10 T6 0,57 S11 R10 T6 0,61 S11 R10 T6 0,95 S1 R1 T1 0,96 S1 R1 T1 0,96 S2 R2
13.2. Expressions for Cortical Bone

13.2.1. Expressions for the Mandible
Apparent density R Axis Young's modulus E (MPa) S-I R E = 0.024 * - 23.93 E = 0.013 * - 13.05 R Sca Ref Tec 0,37 S14 R1 T8 0,54 S14 R1 T8
13.2.2. Expressions for the Tibia

Apparent density = 1 * HU = 1 * HU R Axis Young's modulus E (MPa) S-I B B E = 0.013 * - 3.842 E = 0.00704 * E = 0.06456 * ^ 0.74 R Sca Ref Tec 0,53 S14 R1 T8 0,30 S15 R11 T9 0,30 S15 R11 T9
13.2.3. Expressions for the Humerus

Apparent density R Axis Young's modulus E (MPa) R Sca Ref Tec
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Mimics 14.1 Reference Guide S-I C R E = 0.015 * - 6.326 E = 0.011 * - 8.540 E = 0.011 * - 9.212 0,72 S14 R1 T8 0,66 S14 R1 T8 0,69 S14 R1 T8
13.2.4. Expressions for the Femur

Apparent density R Axis Young's modulus E (MPa) S-I C R E = 0.014 * - 6.142 E = 0.009 * - 4.007 E = 0.010 * - 6.087 R Sca Ref Tec 0,77 S14 R1 T8 0,47 S14 R1 T8 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 M-L S-I P A R B C Anterior-Posterior Medial-Lateral Superior-Inferior parallel to neck axis Average Radial Bending Circumferential
13.3.3. Scanner Types (Sca)

S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 Phillips Tomoscan AV (120 kVp, 150 mAs) Ultrasonic Testing GE 8800 (120 kVp, 240mAs) GE 8800 (120 kVp) Philips Tomoscan AVE1 (120 kV, 100 mA, 1s) Technicare HPS 1440 (130 kVp, 100mA, 4s) / GE 9800 Philips EMI 7070 (140 kVp & 40mA) EMI 7070 (140 kV, 70mA, 3s) EMI 7070 (120 kVp & 50 mA) EMI 7070 (100 kVp & 60 mA) Phillips Tomoscan AV (120 kVp) Siemens Somatom DR3 Phillips Tomoscan AV (120 kVp, 150 mAs) GE 9800 CT (120 kVp, 140 mA, 3s)
13.3.4. Literature Reference (Ref)

R1 R2 R3 Rho, Hobatho, Ashman, 1995 Rho, Hobatho, Ashman, 1997 Lotz, Gerhart, Hayes, 1990
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R4 R5 R6 R7 R8 R9 R10 R11
Esses, Lotz, Hayes, 1989 Pattijn, 2004 Ciarelli, Goldstein, Kuhn, Cody, Brown, 1991 Rho, Zerwekh, Ashman, 1991 Hvid, Bentzen, Linde, Mosekilde, Pongsoipetch, 1989 Bentzen, Hvid, Jrgensen, 1987 Hvid, Bentzen, Linde, Mosekilde, Pongsoipetch, 1989 Snyder, Schneider, 1991
13.3.5. Technique used to determine Youngs modulus (Tec)

T1 T2 T3 T4 T5 T6 T7 T8 T9 Ultrasound velocity measurement at 50kHz Destructive compression test (15% strain) Destructive compression test at high strain rate Non-destructive/destructive compression test Destructive compression test Non-destructive compression test Compression test Ultrasound velocity measurement at 2.25 MHz 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) 157173 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

Name Visible Name of the object. By clicking on the name of the object, it can be renamed. Lists if the object is visible or not by means of glasses. You can change the visibility by clicking on the glasses. Lists if the contour of the objects visible on the 2D images or not by means of glasses. You can change the visibility of the contours by clicking on the glasses. Shows the diameter of the Nerve.
Contour Visible
Diameter
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. 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. Delete Properties Deletes the selected objects. Displays the properties of the selected object:
Copy
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.
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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. The following window will pop up:
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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 and then click on Delete. should appear behind the template name)
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 predefined 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 postoperative 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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Mimics 14.1 Reference Guide Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects 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.
Contour visible
Functions on Cutting Paths

New Properties Allows you to create a new cutting path. 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. 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.
Contour Visible
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 arent 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 youve checked the extensions click OK, the object is now cut AND split at the same time.

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects 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.
Contour visible
Functions on Cutting Lines

Indicate Close Delete Last Extensions Shows the indicate tool and enables you to indicate a cutting line. Closes the cutting line. Deletes the point of the cutting line that was drawn last. 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.

Contour visible
Functions on Cutting Lines
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Indicate Close Delete Last
Shows the indicate tool and enables you to indicate a cutting line. Closes the cutting line. 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

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects All Largest Two largest parts Keep originals parts This way you can choose which parts you want to keep, all cut parts, only the part largest part or only the two largest parts.
Contour visible
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.
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. The following window will appear:
3.4.1. Objects to reposition

First, select the object(s) you want to reposition.
Functions on Objects to Reposition

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible.
Contour visible
Show selected only
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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

Contour visible
Show selected only
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

Contour visible
Show selected only
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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.
The following window will pop up:
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. The following window will appear:
Functions on Objects to Merge
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Mimics 14.1 Reference Guide Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects 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.
Contour visible
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. The following window will appear:
Functions on Objects to Split

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects All Largest Two largest parts Keep originals parts This way you can choose which parts you want to keep, all cut parts, only the part largest part or only the two largest parts.
Contour visible
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.
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. The following window will pop up:
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Functions on Objects to Mirror

Contour visible
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. The following window will pop up:
Functions on Objects to Boolean

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects Operation Keep originals The boolean operation you want to perform on object 1 and 2. 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.
Contour visible
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. The following window will pop up:
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Functions on Objects to Rescale

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects Factor Size You can choose the rescale factor in X, Y and Z direction. 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. If the uniform option is selected, the rescale factor will be the same for X, Y and Z direction. 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.
Contour visible
Uniform
Keep originals
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. 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. 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. Makes the selected objects visible and the unselected objects invisible. Show only selected objects Iterations Smooth factor Compensate shrinkage You can choose how many smoothing iterations will be performed. The smooth factor determines how much smoothing is performed. If the compensate shrinkage setting is enabled, the shrinkage of the object due to the smoothing will be countered. 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.
Contour visible
Keep originals
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. The following window will pop up:
Functions on Objects to Reduce Triangles

Visible Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object. 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.
Contour visible
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Makes the selected objects visible and the unselected objects invisible. 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. 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. 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.
Tolerance
Edge Angle
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 Chapter 2: Mimi Chapter 3: Simon Tutorial that shows how you can import images in Mimics Tutorial that shows how to do a basic segmentation and 3D calculation. Tutorial that shows some advanced segmentation functions to remove artifacts. Tutorial that shows how to use the MedCAD module. Tutorial that shows how to make a mold of a cavity by segmenting the Soft tissue around the cavity. Tutorial that shows how to use the manual import function. Tutorial that shows how to use the FEA module. Tutorial that shows how to use the Simulation module. Tutorial that shows how to use the FEA module for linking to CFD. Tutorial that shows how to combine two meshes.
Chapter 4: Hip Chapter 5: Obturator
Chapter 6: Manual Import Chapter 7: FEA Tutorial Chapter 8: Simulation Tutorial Chapter 9: CFD Tutorial Chapter 10: Assemblies Non-manifold
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 dont 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 dont need all of them. For example, we can decide to delete the images of the project Simon.mcs that dont include parts of mandible or that dont 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 youre 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 isnt 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. Its 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 doesnt 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 pressing the right button; on the right of the 3D window or moving the mouse
select different standard views, like Top, Front, Bottom, by clicking on the button the right of the window;
on
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-lowin the transparency column of the 3D objects tab.
opaque) by clicking the square button
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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 Managements 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 isnt 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 View of the end result

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 dont 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 cant 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 its 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 doesnt apply to the other images in the project. Remark that the threshold weve 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 dont have a grey value within the range will be removed from the mask.
The local threshold range For the moment we dont 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, cant you also add pixels to a mask? Yes, thats 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, its 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 its alright, otherwise youve 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 dont 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, dont 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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Lets 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 youve 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? Its 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 patients 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 dont 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 dont 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

Lets examine what weve obtained so far: the final mandible (with prosthesis), the left prosthesis and the right prosthesis in three different masks. Thats 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 Preparation of the data Thresholding Region growing Calculation of the Polylines Patching of the contours Creation of MedCAD objects Visualization possibilities

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" well 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 Bspline 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 crosssection 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 Preparation of the data Windowing Orientation Thresholding Editing Region growing View of the end result
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 project. . Double click the obturator.mcs
2.2. Windowing
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 cavity. and draw a line in the axial image over the
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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 doesnt apply to other images in the project. Remark that the threshold weve 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 dont 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 510 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 Xdirection, 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. The topics that will be discussed in this tutorial are: Opening the Project Windowing Thresholding Region Growing Calculating a 3D Cutting Splitting Mirroring Repositioning

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
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. The topics that will be discussed in this tutorial are: Opening the Project Calculating a 3D Remeshing the 3D Creating the volume mesh based on the remeshed 3D Material Assignment Exporting the Volumetric Mesh

In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Femur.mcs file.
2. Calculating a 3D
There is already a Yellow mask available in this dataset that will be used to calculate a 3D object. In the Calculate 3D dialog select the High quality setting and click on calculate.
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 nonmanifold 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. The topics that will be discussed in this tutorial are: Importing the images Doing a segmentation Calculating a 3D Object Remeshing the 3D Object Exporting to a Fluent mesh Importing the mesh in Fluent
1. Importing the images

In the File menu, select 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 dont 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 click on the mantle and select wall from the list. tool. To select the wall surface, press left-
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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 dont 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 click on apply.
, make sure the Marked triangles are selected and
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. The topics that will be discussed in this tutorial are: Opening the Project Calculating a 3D Registration of the implant Ostectomy of the femoral neck Remeshing the femur and implant Creating a volume mesh Exporting the remeshed 3D models

In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Femur.mcs file.
2. Calculating a 3D
There is already a yellow mask available in this dataset that will be used to calculate a 3D object. Select the Yellow mask and click on the Calculate 3D icon in the Masks toolbar. In the Calculate 3D dialog select the High quality setting and click on Calculate.
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. TutorialData folder load the Implant.stl. in the toolbar of the STL tab). From the
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 non_manifold_assembly and click on Apply. . Select the
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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 cant 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

Europe (Headquarters)
Materialise Technologielaan 15 3001 Leuven Phone +32 16 39 66 11 mimics@materialise.be
USA & Canada

Materialise 3009 Miller Road Ann Arbor, MI 48103 Phone +1 734 662 5057 mimics@materialise.com
United Kingdom
AMP Technology Centre
Germany
Argelsrieder Feld 10 D- 82234 Oberpfaffenhofen Phone +49 8153 88 12 -0 software@materialise.de
Advanced Manufacturing Park Brunel Way, Catcliffe Sheffield, S60 5WG Phone +44 1142 541 248
software@materialise-rp.co.uk
France
Zone Industrielle 41, Avenue de la Dportation 26100 Romans-sur-Isre Phone +33 4 75 05 00 22 software@materialise.fr
Ukraine
Ul. Raisy Okipnoi 8a
02002 Kiev
Phone +380 44 594 56 10 info@materialise.kiev.ua
China
Room 1803A , BaoAn Mansion No. 800 Dongfang Road, Pudong Shanghai, PRC 200122 Phone + 8621 58312406 software@materialise.com.cn
Japan
Materialise Japan K.K Yokohama Portside Bldg. 2F Sakae-cho 8-1 Kanagawa-ku, Yokohama Phone +81 45 440 4591 software@materialise.co.jp
Malaysia
Materialise Unit 906&907, Block A, Phileo Damansara 2 No 15 Jln. 16/11 46350 Petaling Jaya Selangor Phone +60 3 76652988 software@materialise.com.my
Website:
http://www.materialise.com/mimics
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Mimics 14 Reference Guide

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COMPUTER PROGRAM LICENSE AGREEMENT

10. Privacy notice

PART III .................................................................................................................... 73

PART IV .................................................................................................................. 193

PART V ................................................................................................................... 363

PART VI .................................................................................................................. 467

Mimics 14.1 Reference Guide

Mimics 14.1 Reference Guide

CHAPTER 1: Overview Mimics Modules

Pore Analysis Module

Mimics 14.1 Reference Guide

CHAPTER 2: Installing Mimics

Click Next to proceed.

Mimics 14.1 Reference Guide

Select your region and click Next.

Mimics 14.1 Reference Guide

Mimics 14.1 Reference Guide

Mimics 14.1 Reference Guide

Mimics 14.1 Reference Guide

Mimics 14.1 Reference Guide

1.1.1. Request a key file

Mimics 14.1 Reference Guide

1.1.2. Entering a key file

Mimics 14.1 Reference Guide

1.2.1. Request a License key file

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

Mimics 14.1 Reference Guide

Mimics 14.1 Reference Guide

1.2.2. Enter a key file

1.2.3. Use a floating license server

Mimics 14.1 Reference Guide

The dialog exists out of four sections:

2.1. Password requests

2.2. System Information

Mimics 14.1 Reference Guide

2.4. Overview of Licenses

Mimics 14.1 Reference Guide

CHAPTER 4: Using Help

To display the next page.

To print the current page.

PART II General Information

Mimics 14.1 Reference Guide

CHAPTER 1: User Interface

Image Axial Sagittal Coronal 3D view Parallel Cross-sectional

and and and and and and and and

Mimics 14.1 Reference Guide

4.1. Toggle transparency

Clipping in the Axial Plane

Clipping in the Sagittal Plane

Combined Axial and Sagittal Clipping Planes

Clipping along two axial and a sagittal plane

Clipping along the axial and sagittal plane

Mimics 14.1 Reference Guide

Full slice texturing

4.3. Volume rendering

Defining the opacity

Click left on a line to add an extra point

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

Defining the color

4.4. Show reference planes

Mimics 14.1 Reference Guide