Klinik und Poliklinik für Mund-Kiefer-Gesichtschirurgie der Technischen Universität München Klinikum rechts der Isar (Direktor: Univ.-Prof. Dr. Dr. Dr. h.c. (UMF Temeschburg) H.-H. Horch) 3D Interactive Segmentation – First Applications for Computer-Aided Craniofacial Surgical Planning Lutz Ritter Vollständiger Abdruck der von der Fakultät für Medizin der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Medizin genehmigten Dissertation. Vorsitzender: Univ.-Prof. D. Neumeier Prüfer der Dissertation: 1. Prof. Dr. Dr. H.-F. Zeilhofer, Universität Basel / Schweiz 2. Univ.-Prof. Dr. Dr. Dr. h.c. (UMF Temeschburg) H-H. Horch Die Disseration wurde am 04.03.2004 bei der Technischen Universität München eingereicht und durch die Fakultät für Medizin am 11.05.2005 angenommen. 1 Summary ............................................................................................................1 2 Introduction ......................................................................................................2 3 Rationale ............................................................................................................5 4 Related Work.....................................................................................................8 4.1 3D Slicer ...................................................................................................................9 4.2 Analyze ...................................................................................................................12 4.3 Amira......................................................................................................................14 4.4 Mimics ....................................................................................................................17 4.5 3D Interactive Segmentation..................................................................................18 5 Material and Methods ...................................................................................19 5.1 Computer Tomography...........................................................................................19 5.1.1 Technique ...........................................................................................................................................20 5.1.2 Scanners and Protocols ..................................................................................................................21 5.1.3 Image Quality ...................................................................................................................................22 5.1.4 Implications of Image Acquisition on 3D Model Generation ..............................................23 5.2 Patient Data ...........................................................................................................24 5.3 Computer Hardware ..............................................................................................25 5.4 Julius - A General Software Framework ...............................................................26 5.5 Data Management ..................................................................................................27 5.5.1 Image Transfer .................................................................................................................................27 5.5.2 Image Formats..................................................................................................................................29 5.5.3 Criteria For Efficient Data Management .................................................................................30 5.6 Image Enhancement...............................................................................................31 5.6.1 General Aspects................................................................................................................................31 5.6.2 Criteria for Image Enhancement of Medical CT Images .....................................................32 5.6.3 Low Pass Filtering...........................................................................................................................33 5.6.4 Median Filtering ..............................................................................................................................34 5.6.5 Markov Random Fields Filtering................................................................................................34 5.6.6 Anisotropic Diffusion Filtering ....................................................................................................35 5.6.7 Metal Artifact Removal Filter......................................................................................................35 5.7 Visualization ..........................................................................................................36 5.7.1 General Aspects................................................................................................................................36 5.7.2 2D Visualization...............................................................................................................................38 5.7.3 3D Volume Visualization ...............................................................................................................39 5.7.4 3D Surface Visualization ...............................................................................................................40 5.7.5 Criteria For Efficient Visualization............................................................................................41 5.8 Image Segmentation...............................................................................................42 5.8.1 General Aspects................................................................................................................................42 5.8.2 Threshold Segmentation................................................................................................................43 5.8.3 Region Growing Segmentation ....................................................................................................45 5.8.4 Manual Segmentation ....................................................................................................................45 5.9 Evaluation of Segmentation Algorithms................................................................47 5.9.1 Procedure............................................................................................................................................47 5.9.2 Hausdorff Distance (Maximum Surface Distance) ................................................................48 5.9.3 Mean Distance ..................................................................................................................................49 -ii- 6 Results ..............................................................................................................50 6.1 Data Management ..................................................................................................50 6.2 Image Enhancement...............................................................................................53 6.2.1 Low Pass Filtering...........................................................................................................................53 6.2.2 Median Filtering ..............................................................................................................................55 6.2.3 Anisotropic Diffusion Filtering ....................................................................................................56 6.2.4 Markov Random Field Filtering..................................................................................................57 6.2.5 Metal Artifact Removal..................................................................................................................59 6.3 Visualization ..........................................................................................................60 6.3.1 Volume Visualization......................................................................................................................60 6.3.2 3D Model Reconstruction...............................................................................................................61 6.4 Segmentation..........................................................................................................63 6.5 Evaluation of Segmentation Algorithms................................................................64 6.6 A Processing Pipeline For The Generation of 3D Surface Models .........................67 7 Discussion ........................................................................................................69 7.1 Data Management ..................................................................................................69 7.2 Image Enhancement...............................................................................................69 7.3 Segmentation..........................................................................................................70 7.4 Evaluation of 3D Interactive Segmentation...........................................................72 7.5 3D Model Reconstruction .......................................................................................74 7.6 Julius – a General Software Framework ...............................................................75 8 Conclusion .......................................................................................................76