Contents

Contents vi

1 Introduction 1 1.1 OsiriX ...... 1 1.1.1 About DICOM ...... 1 1.1.2 History ...... 1 1.2 Indications For Use ...... 4 1.3 Contraindications ...... 4 1.4 Reporting A Problem ...... 4 1.4.1 How to report a problem ...... 4 1.5 Requirements ...... 6 1.6 Installation ...... 7 1.7 Mac OS X ...... 8 1.7.1 Mouse ...... 8 1.7.2 Keyboard Shortcuts ...... 8 1.7.3 Window Toolbar ...... 10 1.7.3.1 Toolbar Customization ...... 10 1.8 Plugins ...... 11 1.8.0.2 Plugins Development ...... 11

2 Preferences 13 2.1 Basics ...... 14 2.1.1 General ...... 14 2.1.1.1 Security ...... 14 2.1.1.2 DICOM Toolkits ...... 15 2.1.1.3 DICOM Compression ...... 15 2.1.1.4 Check version ...... 15 2.1.1.5 DICOM Editing ...... 15 2.1.2 Database ...... 16 2.1.2.1 File Management ...... 16 2.1.2.2 Database Display ...... 17 2.1.2.3 Comments field ...... 17 2.1.2.4 Series Parsing ...... 18 2.1.2.5 Sort Series By ...... 18 2.1.2.6 Sort Images By ...... 18 2.1.2.7 Database Auto-Cleaning ...... 19 2.1.2.8 Reports ...... 19 2.1.3 CD/DVD ...... 19 2.1.4 Protocols ...... 20 2.2 Display ...... 22 2.2.1 Viewers ...... 22 2.2.1.1 TIFF, JPEG, QuickTime, DICOM Export ...... 22

vi CONTENTS vii

2.2.1.2 Screens & Window size ...... 23 2.2.1.3 Miscellaneous ...... 23 2.2.2 3D ...... 25 2.2.2.1 Best Rendering Button ...... 25 2.2.2.2 Default View Size ...... 26 2.2.2.3 Misc ...... 26 2.2.3 PET ...... 26 2.2.3.1 CLUT ...... 26 2.2.3.2 Opacity Table ...... 26 2.2.3.3 Mouse Windowing Mode ...... 26 2.2.3.4 Window Level & Width ...... 27 2.2.3.5 Fusion Type ...... 28 2.2.4 Hot Keys ...... 28 2.2.5 Annotations ...... 30 2.3 Sharing ...... 31 2.3.1 Listener ...... 31 2.3.1.1 Basic Settings ...... 31 2.3.1.2 Mac OS X User Session ...... 33 2.3.1.3 DICOM Multi-Threading ...... 33 2.3.1.4 DICOM Communications Time-out ...... 33 2.3.1.5 DICOM TLS Listener ...... 33 2.3.1.6 Incoming Files Indexing Interval ...... 33 2.3.1.7 File compression ...... 33 2.3.1.8 Unreadable Files ...... 34 2.3.1.9 Activate OsiriX database sharing ...... 34 2.3.1.10 Bonjour ...... 34 2.3.1.11 Incoming and Outcoming files are linked to the de- fault database ...... 34 2.3.1.12 Anonymization ...... 34 2.3.1.13 DICOM Network Events Logs ...... 34 2.3.1.14 Server Mode ...... 35 2.3.1.15 C–GET SCP ...... 35 2.3.1.16 XML–RPC Server ...... 35 2.3.2 Locations ...... 35 2.3.2.1 DICOM Nodes (DICOM Q&R and DICOM Send) . . 35 2.3.2.2 Shared OsiriX Databases ...... 38 2.3.2.3 Local OsiriX Databases ...... 38 2.3.3 Routing ...... 38 2.3.4 DICOM Print ...... 40 2.3.5 Web Server ...... 40

3 Database 43 3.1 The Database Window ...... 43 3.1.1 Toolbar ...... 44 3.1.1.1 2D Viewer ...... 44 3.1.1.2 4D Viewer ...... 45 3.1.1.3 Album & Sources ...... 45 3.1.1.4 Anonymize ...... 45 3.1.1.5 Burn ...... 45 3.1.1.6 CD-Rom ...... 46 3.1.1.7 Delete ...... 46 3.1.1.8 Export ...... 46 3.1.1.9 iDisk Get ...... 46 viii CONTENTS

3.1.1.10 iDisk Send ...... 46 3.1.1.11 Import ...... 46 3.1.1.12 Meta-Data ...... 46 3.1.1.13 Search ...... 46 3.1.1.14 Query ...... 46 3.1.1.15 Report ...... 47 3.1.1.16 ROIs & Keys ...... 47 3.1.1.17 Search ...... 47 3.1.1.18 Send ...... 47 3.1.1.19 Time Interval ...... 47 3.1.2 Study List ...... 47 3.1.3 Series List ...... 50 3.1.4 Series Preview ...... 51 3.1.5 The side drawer ...... 51 3.1.5.1 The Albums ...... 51 3.1.5.2 The Sources ...... 53 3.1.5.3 The Activity Panel ...... 54 3.2 Files Management ...... 54 3.2.1 DICOM Files ...... 54 3.2.1.1 Meta-Data Window ...... 54 3.2.2 Importing Images ...... 55 3.2.3 Burning DICOM CD/DVD ...... 56 3.2.4 Series Parsing ...... 57 3.2.5 The Database Folder ...... 58 3.2.6 Rebuilding the database ...... 59 3.3 Database Structure ...... 60 3.3.1 Study Level ...... 60 3.3.2 Series Level ...... 61 3.3.3 Image Level ...... 62 3.3.3.1 Compression of the SOPInstanceUID ...... 63 3.3.4 Album ...... 64 3.4 Managing multiple databases ...... 64 3.4.1 Exchanging studies between database ...... 64 3.5 Reports ...... 65 3.5.1 Report Template ...... 66 3.5.2 Report Archiving ...... 67 3.5.3 Report Sharing ...... 67 3.5.4 DICOM SR ...... 67

4 Communications 69 4.1 General Concepts ...... 69 4.1.1 Importing and Receiving Data ...... 69 4.1.2 Sending Data ...... 69 4.1.3 Sharing Data ...... 70 4.2 DICOM Communications ...... 71 4.2.1 Introduction ...... 71 4.2.2 DICOM Protocols ...... 71 4.2.2.1 Store Service Class Provider (C–STORE SCP) - DI- COM Listener ...... 72 4.2.2.2 Store Service Class User (C–STORE SCU) - DICOM Send ...... 73 4.2.2.3 Find Service Class Provider (C–FIND SCP) ...... 73 4.2.2.4 Find Service Class User (C–FIND SCU) ...... 74 CONTENTS ix

4.2.2.5 Move Service Class Provider (C–MOVE SCP) . . . . . 75 4.2.2.6 Move Service Class User (C–MOVE SCU) ...... 75 4.2.2.7 Get Service Class Provider (C–GET SCP) ...... 76 4.2.2.8 Get Service Class User (C–GET SCU) ...... 76 4.2.2.9 Print Service Class User (C–PRINT SCU) ...... 77 4.2.3 DICOM Listener ...... 77 4.2.4 DICOM Nodes ...... 78 4.2.5 Query & Retrieve ...... 80 4.2.6 Auto-Query & Retrieve ...... 81 4.2.7 Auto–routing ...... 81 4.2.8 Setting up OsiriX as a storage server (PACS) ...... 82 4.2.9 Security ...... 82 4.2.10 Synchronize and Archive ...... 83 4.2.11 WADO ...... 84 4.2.12 DICOM Conformance Statement ...... 84 4.3 Database Sharing ...... 84 4.4 Network Logs ...... 84 4.5 HTTP Web Server ...... 85 4.5.1 Notifications ...... 88 4.5.2 Security ...... 88 4.5.3 Users Management ...... 89 4.5.4 Web Pages Customization ...... 90 4.6 XML–RPC ...... 90 4.6.1 XML–RPC Server Activation & Setup ...... 91 4.6.2 Supported XML–RPC Messages in OsiriX ...... 91 4.6.3 XML–RPC Messages format ...... 94 4.6.4 XML–RPC Response format ...... 94 4.6.5 Extending the XML–RPC capabilities of OsiriX ...... 96 4.7 Building a JPEG 2000 network ...... 97 4.7.1 Set-up ...... 98 4.7.1.1 OsiriX Server ...... 99 4.7.1.2 OsiriX Workstations ...... 99 4.7.2 Conclusion ...... 100

5 The 2D Viewer 103 5.1 The Anatomy of the 2D Viewer ...... 103 5.1.1 Toolbar ...... 103 5.1.1.1 2D/3D Button ...... 103 5.1.1.2 3D Panel ...... 104 5.1.1.3 3D Position ...... 104 5.1.1.4 4D Player ...... 104 5.1.1.5 Browse ...... 104 5.1.1.6 Cobb’s Angle ...... 104 5.1.1.7 Convolution Filters ...... 104 5.1.1.8 Database ...... 104 5.1.1.9 Delete ...... 104 5.1.1.10 Email ...... 104 5.1.1.11 Flip ...... 104 5.1.1.12 Flip Horizontal ...... 105 5.1.1.13 Flip Vertical ...... 105 5.1.1.14 Fusion ...... 105 5.1.1.15 Growing ...... 105 5.1.1.16 iChat ...... 105 x CONTENTS

5.1.1.17 iPhoto ...... 105 5.1.1.18 Key Images ...... 105 5.1.1.19 Meta-Data ...... 105 5.1.1.20 Mouse button function ...... 106 5.1.1.21 Movie Export ...... 106 5.1.1.22 Navigator ...... 106 5.1.1.23 Orientation ...... 107 5.1.1.24 Patient ...... 107 5.1.1.25 Print ...... 107 5.1.1.26 Propagate ...... 107 5.1.1.27 Rate ...... 107 5.1.1.28 Report ...... 107 5.1.1.29 Reset ...... 107 5.1.1.30 Revert ...... 107 5.1.1.31 RGB Factors ...... 107 5.1.1.32 ROI Manager ...... 108 5.1.1.33 Save as DICOM ...... 108 5.1.1.34 Send ...... 108 5.1.1.35 Series ...... 108 5.1.1.36 Set Pixels ...... 108 5.1.1.37 Shutter ...... 108 5.1.1.38 Status & Comments ...... 108 5.1.1.39 Subtraction ...... 108 5.1.1.40 SUV ...... 108 5.1.1.41 Sync ...... 108 5.1.1.42 Thick Slab ...... 109 5.1.1.43 Tile ...... 109 5.1.1.44 WL/WW, CLUT & Opacity ...... 109 5.2 Displaying images ...... 109 5.2.1 Displaying a series ...... 109 5.2.1.1 Propagate Settings In a Series ...... 109 5.2.2 Displaying multiple series ...... 110 5.2.2.1 Tiling & Magnetic Windows ...... 110 5.2.2.2 Propagate Settings ...... 110 5.2.2.3 Synchronization ...... 111 5.2.2.4 Reference Lines ...... 111 5.3 Navigating between Studies and Series ...... 112 5.3.1 Switching image series ...... 112 5.3.2 Switching patients ...... 112 5.3.3 Switching back to database browser ...... 113 5.3.4 The Preview list ...... 113 5.4 Workflow ...... 114 5.4.1 Workspace ...... 114 5.4.2 Key Images ...... 115 5.4.3 Printing ...... 115 5.4.4 Email ...... 116 5.4.5 iChat ...... 117 5.4.6 Magnifying Lens ...... 118 5.4.7 Image Export ...... 119 5.4.8 Movie Export ...... 120 5.4.9 DICOM Secondary Captures ...... 121 5.5 Viewing Tools ...... 123 5.5.1 Mouse Tools ...... 123 CONTENTS xi

5.5.1.1 Window Level & Width Tool ...... 123 5.5.1.2 Pan Tool ...... 123 5.5.1.3 Zoom Tool ...... 123 5.5.1.4 Rotate Tool ...... 123 5.5.1.5 Scroll Tool ...... 123 5.5.2 Window Level & Width ...... 124 5.5.3 Color Look Up Table ...... 124 5.5.4 Opacity ...... 126 5.5.5 Thick Slab ...... 126 5.5.6 Orientation ...... 127 5.5.7 Navigator ...... 127 5.5.8 Image Subtraction ...... 128 5.5.9 Image Fusion ...... 129 5.5.9.1 3D Position ...... 131 5.5.10 Series Registration ...... 132 5.5.11 Image Stitching ...... 132 5.5.12 Annotations ...... 133 5.5.13 Shutter Tool ...... 134 5.5.14 Convolution Filters ...... 134 5.5.14.1 Smoothing & Blurring Filters ...... 136 5.5.14.2 Sharping Filters ...... 139 5.5.14.3 Edges Detection Filters ...... 140 5.5.14.4 Embossing Filters ...... 142 5.5.15 Using a 12-bit Totoku Monitor ...... 144 5.6 Quantification Tools ...... 144 5.6.1 The ROIs ...... 144 5.6.1.1 Length ROI ...... 145 5.6.1.2 Angle ROI ...... 145 5.6.1.3 Rectangle ROI ...... 145 5.6.1.4 Oval ROI ...... 145 5.6.1.5 Text ROI ...... 146 5.6.1.6 Arrow ROI ...... 146 5.6.1.7 Closed Polygon ROI ...... 146 5.6.1.8 Opened Polygon ROI ...... 146 5.6.1.9 Pencil ROI ...... 146 5.6.1.10 Point ROI ...... 147 5.6.1.11 Brush ROI ...... 147 5.6.1.12 Axis ROI ...... 147 5.6.1.13 Dynamic Angle ROI ...... 147 5.6.1.14 Repulsor Tool ...... 147 5.6.1.15 ROI Selector Tool ...... 148 5.6.1.16 ROI Info Box ...... 148 5.6.1.17 ROI Info Panel ...... 149 5.6.1.18 ROI naming ...... 150 5.6.1.19 ROI selection ...... 150 5.6.1.20 ROI deletion ...... 151 5.6.1.21 ROI Spline Rendering ...... 151 5.6.1.22 3D ROIs and Volume ...... 151 5.6.1.23 Angle of Cobb ...... 152 5.6.2 Region Growing ...... 154 5.6.3 Set Pixels Values ...... 155 5.6.4 SUV ...... 156 5.7 Reconstruction Tools ...... 159

CONTENTS xiii

7.3.2 Exporting QuickTime VR Movies ...... 183

8 The 3D Surface Rendering 185 8.1 The Anatomy of the SR Viewer ...... 185 8.1.1 Toolbar ...... 185 8.1.1.1 Surface Settings ...... 186 8.1.1.2 Fusion Surface Settings ...... 186 8.1.1.3 Stereo ...... 186 8.1.1.4 Orientation Cube ...... 187 8.1.1.5 Movie Export ...... 187 8.1.1.6 iPhoto ...... 187 8.1.1.7 Export QTVR ...... 188 8.1.1.8 Export 3D-SR ...... 188 8.1.1.9 Orientations ...... 188 8.1.1.10 Mouse button function ...... 189 8.1.1.11 ROI Manager ...... 189 8.1.1.12 Fly Through ...... 189 8.1.1.13 Show/Hide 3D Points ...... 190 8.1.1.14 Perspective ...... 190 8.1.1.15 Reset ...... 191 8.1.1.16 Save as DICOM ...... 191 8.1.1.17 Background Color ...... 191 8.2 3D Viewing Functions ...... 191 8.2.1 Surface Rendering ...... 191 8.2.2 3D Surface Rendering Engine ...... 192 8.2.3 Projections mode ...... 192 8.2.4 Sculpting 3D images ...... 193 8.2.5 Image Fusion ...... 193 8.2.6 4D Dataset ...... 193 8.2.7 ROIs ...... 193 8.3 Exporting 3D Images ...... 194 8.3.1 Exporting QuickTime Movies ...... 195 8.3.2 Exporting QuickTime VR Movies ...... 195

9 The 3D Endoscopy 197 9.1 The Anatomy of the Endoscopy Viewer ...... 197 9.1.1 Toolbar ...... 197 9.1.1.1 Save as DICOM ...... 198 9.1.1.2 3D Mouse button function (3D View) ...... 198 9.1.1.3 MPR Mouse button function (MPR Views) ...... 198 9.1.1.4 Fly Through (3D View) ...... 199 9.1.1.5 Path Assistant (3D View / MPR Views) ...... 199 9.1.1.6 3D WL/WW (3D View) ...... 200 9.1.1.7 MPR WL/WW (MPR Views) ...... 200 9.1.1.8 3D CLUT (3D View) ...... 200 9.1.1.9 MPR CLUT (MPR Views) ...... 200 9.1.1.10 3D Opacity (3D View) ...... 200 9.1.1.11 MPR Opacity (MPR Views) ...... 200 9.1.1.12 Shadings (3D View) ...... 200 9.1.1.13 Level of Detail (3D View) ...... 200 9.2 Endoscopy Viewer Functions ...... 200 9.2.1 Endoscopy Viewer Engine ...... 201 9.2.2 Cross reference lines ...... 201 xiv CONTENTS

9.2.3 Image Fusion ...... 201 9.2.4 4D Dataset ...... 201 9.2.5 ROIs ...... 201 9.2.6 Path Assistant ...... 201 9.3 Exporting MPR Images ...... 202

10 The 3D MPR 203 10.1 The Anatomy of the 3D MPR Viewer ...... 203 10.1.1 Toolbar ...... 203 10.1.1.1 Mouse Tools ...... 204 10.1.1.2 WL/WW ...... 204 10.1.1.3 CLUT ...... 204 10.1.1.4 Opacity ...... 204 10.1.1.5 Level of Details ...... 204 10.1.1.6 Best Rendering ...... 205 10.1.1.7 Thick Slab ...... 205 10.1.1.8 Fusion ...... 205 10.1.1.9 Shading ...... 205 10.1.1.10 4D Player ...... 205 10.1.1.11 Reset ...... 206 10.1.1.12 Save as DICOM ...... 206 10.1.1.13 Movie Export ...... 207 10.1.1.14 Axis Colors ...... 207 10.1.1.15 Axis ...... 207 10.1.1.16 Mouse Position ...... 207 10.1.1.17 Sync Zoom ...... 207 10.2 3D MPR Viewing Functions ...... 208 10.2.1 3D MPR Engine ...... 208 10.2.2 Plane Position ...... 209 10.2.3 Cross reference lines ...... 209 10.2.4 Thick Slab ...... 209 10.2.5 Image Fusion ...... 210 10.2.6 4D Dataset ...... 210 10.2.7 ROIs ...... 211 10.3 Exporting MPR Images ...... 211 10.3.1 Exporting QuickTime Movies ...... 212

11 The 2D Orthogonal MPR 213 11.1 The Anatomy of the 2D Orthogonal MPR Viewer ...... 213 11.1.1 Toolbar ...... 213 11.1.1.1 WL/WW ...... 213 11.1.1.2 CLUT ...... 213 11.1.1.3 Opacity ...... 214 11.1.1.4 Thick Slab ...... 214 11.1.1.5 4D Player ...... 214 11.1.1.6 Mouse button function ...... 214 11.1.1.7 Save as DICOM ...... 215 11.1.1.8 Email ...... 215 11.1.1.9 Same widths / heights ...... 215 11.1.1.10 Reset ...... 215 11.1.1.11 Flip Volume ...... 216 11.1.1.12 3D Panel ...... 216 11.1.1.13 Fusion ...... 216 CONTENTS xv

11.1.1.14 3D Pos ...... 216 11.2 2D Orthogonal MPR Viewing Functions ...... 216 11.2.1 2D Orthogonal MPR Engine ...... 216 11.2.2 Cross reference lines ...... 216 11.2.3 Thick Slab ...... 216 11.2.4 Image Fusion ...... 217 11.2.5 4D Dataset ...... 218 11.2.6 ROIs ...... 218 11.3 Exporting MPR Images ...... 219 11.3.1 Exporting QuickTime Movies ...... 219

12 The 2D Curved MPR 221 12.0.2 Curved MPR Engine ...... 221 12.0.3 Curved MPR in a single plane ...... 221 12.0.4 Curved MPR in multiple images ...... 222 12.0.5 Image Fusion ...... 223 12.0.6 4D Dataset ...... 223

13 The Menus 225 13.1 The OsiriX Menu ...... 225 13.1.1 About OsiriX ...... 225 13.1.2 Preferences...... 225 13.1.3 Check for Updates ...... 226 13.1.4 Hide OsiriX ...... 226 13.1.5 Hide Others ...... 226 13.1.6 Quit OsiriX ...... 226 13.2 The File Menu ...... 226 13.2.1 Show Database Window ...... 227 13.2.2 New Database Folder...... 227 13.2.3 Open Database Folder...... 227 13.2.4 Report ...... 227 13.2.4.1 Open Report ...... 227 13.2.4.2 Delete Report ...... 227 13.2.5 Import ...... 227 13.2.5.1 Import Files...... 228 13.2.5.2 Import Image from URL...... 228 13.2.5.3 Import Raw Data ...... 228 13.2.6 Export ...... 228 13.2.6.1 Export to DICOM Network Node ...... 228 13.2.6.2 Export to QuickTime ...... 228 13.2.6.3 Export to QuickTime VR ...... 228 13.2.6.4 Export to JPEG ...... 228 13.2.6.5 Export to Raw ...... 228 13.2.6.6 Export to TIFF ...... 228 13.2.6.7 Export to DICOM file(s) ...... 229 13.2.6.8 Export to Email ...... 229 13.2.6.9 Export to iPhoto ...... 229 13.2.6.10 Export to iDisk ...... 229 13.2.6.11 Export Displayed Database List as...... 229 13.2.7 Burn...... 229 13.2.8 Anonymize...... 229 13.2.9 Copy Linked Files to Database folder ...... 230 13.2.10 Search ...... 230 xvi CONTENTS

13.2.11 Merge Selected Study ...... 230 13.2.12 Delete Selected Exam ...... 230 13.2.13 Compress selected DICOM in JPEG ...... 230 13.2.14 Decompress selected DICOM ...... 230 13.2.15 Rebuild Entire Database...... 230 13.2.16 Rebuild SQL Index File...... 230 13.2.17 Rebuild Selected Thumbnails ...... 230 13.2.18 Close Window ...... 230 13.2.19 Page Setup...... 231 13.2.20 Print...... 231 13.2.21 DICOM Print...... 231 13.3 The Network Menu ...... 231 13.3.0.1 Export to DICOM Network Node ...... 231 13.3.1 Query / Retrieve...... 231 13.3.2 Query / Retrieve Selected Patient...... 232 13.3.3 Auto Query / Retrieve...... 232 13.3.4 Abort Incoming DICOM Processes (Store-SCU) ...... 232 13.3.5 Network Logs ...... 232 13.4 The Edit Menu ...... 232 13.4.1 Undo ...... 232 13.4.2 Redo ...... 232 13.4.3 Cut ...... 233 13.4.4 Copy ...... 233 13.4.5 Paste ...... 233 13.4.6 Clear ...... 233 13.4.7 Select All ...... 233 13.5 The Format Menu ...... 233 13.5.1 Customize Toolbar...... 233 13.5.2 Fullscreen ...... 233 13.5.3 Font ...... 233 13.5.3.1 Show Fonts ...... 233 13.5.3.2 Bold ...... 233 13.5.3.3 Italic ...... 234 13.5.3.4 Bigger ...... 234 13.5.3.5 Smaller ...... 234 13.5.3.6 Kern ...... 234 13.5.3.7 Ligature ...... 234 13.5.3.8 Baseline ...... 234 13.5.3.9 Show Colors ...... 234 13.6 The 2D Viewer Menu ...... 235 13.6.1 Next series ...... 235 13.6.2 Previous series ...... 235 13.6.3 Convert Between BW / RGB ...... 236 13.6.4 Reset Image View ...... 236 13.6.5 Revert series ...... 236 13.6.6 Sort By ...... 236 13.6.7 Orientation ...... 236 13.6.7.1 Flip Image Horizontal ...... 236 13.6.7.2 Flip Image Vertical ...... 236 13.6.7.3 Rotation 0 degrees ...... 236 13.6.7.4 Rotation 90 degrees ...... 236 13.6.7.5 Rotation 180 degrees ...... 236 13.6.8 Calibrate resolution ...... 236 CONTENTS xvii

13.6.9 3D Position Panel ...... 237 13.6.10 Navigator Panel ...... 237 13.6.11 Flip Series ...... 238 13.6.12 Use VOI LUT if Available ...... 238 13.6.13 Display DICOM Overlays ...... 238 13.6.14 DICOM Meta-Data ...... 238 13.6.15 Fuse/De-Fuse PET/SPECT-CT ...... 238 13.6.16 Flatten Fused Image ...... 238 13.6.17 Broadcast Viewer via iChat ...... 238 13.6.18 Propagate settings between series ...... 238 13.6.19 Don’t propagate WL/WW between series ...... 238 13.6.20 Propagate settings in current series ...... 239 13.6.21 Sync Series (same study) ...... 239 13.6.22 Sync Series (different studies) at current position ...... 239 13.6.23 Key Image ...... 239 13.6.24 Mark All Images as Key Images ...... 239 13.6.25 Unmark All Images as Key Images ...... 239 13.6.26 Mark All ROIs Images as Key Images ...... 239 13.6.27 Find Next Key Image ...... 239 13.6.28 Find Previous Key Image ...... 239 13.6.29 Subtraction ...... 240 13.6.29.1 Subtract ...... 240 13.6.29.2 New Mask ...... 240 13.6.29.3 Sharpen ...... 240 13.6.29.4 Pixel Shift ...... 240 13.6.29.5 Contrast Down ...... 240 13.6.29.6 Contrast Default ...... 240 13.6.29.7 Contrast Up ...... 240 13.6.29.8 Brightness Down ...... 240 13.6.29.9 Brightness Default ...... 240 13.6.29.10Brightness Up ...... 240 13.6.29.11Sum Less ...... 241 13.6.29.12No Sum ...... 241 13.6.29.13Sum More ...... 241 13.6.30 Annotations ...... 241 13.6.30.1 None ...... 241 13.6.30.2 Graphic Only ...... 241 13.6.30.3 Basic (No Name) ...... 241 13.6.30.4 Full (Patient Name) ...... 241 13.6.30.5 Plugin Only ...... 241 13.6.30.6 Display Cross Reference Lines ...... 241 13.6.31 Window Width & Level ...... 241 13.6.32 Color Look Up Table ...... 242 13.6.33 Color Look Up Table Bar ...... 242 13.6.34 Opacity ...... 242 13.6.35 Convolution Filters ...... 242 13.6.36 Apply Convolution Filters to raw data ...... 242 13.6.37 Image Tiling ...... 242 13.6.38 Windows Tiling ...... 242 13.6.39 Save Workspace State ...... 242 13.6.40 Load Workspace State ...... 242 13.6.41 Reset Workspace State ...... 242 13.7 The 3D Viewer Menu ...... 243 xviii CONTENTS

13.7.1 3D MPR ...... 243 13.7.2 2D Curved MPR ...... 243 13.7.3 2D Orthogonal MPR ...... 243 13.7.4 3D MIP ...... 243 13.7.5 3D Volume Rendering ...... 244 13.7.6 3D Surface Rendering ...... 244 13.7.7 3D Endoscopy ...... 244 13.7.8 Reset to initial view ...... 244 13.7.9 Revert series ...... 244 13.7.10 Coronal View ...... 244 13.7.11 Left Sagittal View ...... 244 13.7.12 Right Sagittal View ...... 244 13.7.13 Axial View ...... 245 13.7.14 Add FlyThru Point ...... 245 13.7.15 Remove FlyThru Point ...... 245 13.7.16 Reset FlyThru Path ...... 245 13.7.17 Scissor Editing ...... 245 13.7.18 Select 3D Preset...... 245 13.7.19 Save current State as 3D Preset...... 245 13.8 The ROI Menu ...... 246 13.8.1 Import ROI(s)...... 246 13.8.2 Save Selected ROI(s)...... 246 13.8.3 Save All ROIs of this Series...... 246 13.8.4 Delete All ROIs in this Series ...... 246 13.8.5 Delete All ROIs with Same Name as Selected ROI ...... 246 13.8.6 Select All ROIs in this Series ...... 246 13.8.7 Deselect All ROIs in this Series ...... 247 13.8.8 ROI manager...... 247 13.8.9 ROI info...... 247 13.8.10 ROI Rename...... 247 13.8.11 Set Default ROI Name...... 247 13.8.12 Display Info Only when ROI Selected ...... 247 13.8.13 Display Name Only ...... 247 13.8.14 Increase Thickness ...... 247 13.8.15 Decrease Thickness ...... 247 13.8.16 Increase Font Size ...... 247 13.8.17 Decrease Font Size ...... 247 13.8.18 Histogram of Selected ROI...... 247 13.8.19 Create Layer from Selected ROI ...... 247 13.8.20 ROI Volume ...... 247 13.8.20.1 Compute Volume...... 247 13.8.20.2 Generate Missing ROIs ...... 248 13.8.20.3 Delete Generated ROIs ...... 248 13.8.20.4 Erase content ...... 248 13.8.20.5 Restore content ...... 248 13.8.21 Propagate Selected ROI...... 248 13.8.22 Propagate Selected ROI to current Thick Slab ...... 248 13.8.23 Group Selected ROIs ...... 248 13.8.24 Ungroup Selected ROIs ...... 248 13.8.25 Lock Selected ROIs ...... 248 13.8.26 Unlock Selected ROIs ...... 248 13.8.27 Make Selected ROIs Unselectable ...... 248 13.8.28 Make All ROIs Selectable ...... 248 CONTENTS xix

13.8.29 Set Pixel Value to...... 248 13.8.30 Grow Region (2D/3D Segmentation)...... 249 13.8.31 Brush ROIs ...... 249 13.9 The Plugins Menu ...... 249 13.9.1 Image Filters ...... 249 13.9.2 ROI Tools ...... 249 13.9.3 Others ...... 250 13.9.4 Database ...... 250 13.9.5 Plugins Manager...... 250 13.10The Window Menu ...... 250 13.10.1 Minimize ...... 250 13.10.2 Resize Window ...... 250 13.10.3 Tile Windows ...... 250 13.10.4 Close All Viewers ...... 250 13.10.5 Bring All to Front ...... 250 13.11The Help Menu ...... 251 13.11.1 Search ...... 251 13.11.2 Email Project Lead ...... 251 13.11.3 OsiriX Web site ...... 251 13.11.4 OsiriX Discussion Group ...... 251 13.11.5 OsiriX Help ...... 251

A Security 253 A.1 DICOM TLS ...... 253 A.1.1 Authentication ...... 253 A.1.2 OsiriX TLS DICOM Listener Setup ...... 253 A.2 OsiriX Secure Web Server Setup ...... 257 A.3 Creating a Self-Signed Certificate ...... 260 A.4 Requesting a Certificate from a Certification Authority ...... 266 A.4.1 Real-world example ...... 269 A.5 Changing the Trust Settings of a Certificate ...... 277

B DICOM Conformance Statement 281 B.1 Conformance Statement Overview ...... 281 B.1.1 Image, Waveform, Measurements and Reports Transfer/Storing 281 B.1.2 Query/Retrieve ...... 282 B.1.3 Print Management ...... 282 B.1.4 Media Services ...... 282 B.2 Introduction ...... 282 B.2.1 Audience ...... 282 B.3 Networking ...... 283 B.3.1 Implementation Model ...... 283 B.3.1.1 Application Data Flow ...... 283 B.3.1.2 Functional Definition of Application Entities ...... 283 B.3.1.3 Sequencing of Real World Activities ...... 284 B.3.2 AE Specifications ...... 285 B.3.2.1 Store-SCU ...... 285 B.3.2.2 Store-SCP ...... 287 B.3.2.3 Print-SCU ...... 290 B.3.2.4 Find-SCU, Get-SCU, Move-SCU ...... 290 B.3.2.5 Find-SCP, Get-SCP, Move-SCP ...... 294 B.3.3 Network Interfaces ...... 297 B.3.3.1 Physical Network Interfaces ...... 297 xx CONTENTS

B.3.3.2 Additional Protocols ...... 297 B.3.4 Configuration ...... 297 B.3.4.1 AE Title/Presentation Address Mapping ...... 297 B.3.4.2 Parameters ...... 298 B.4 Media Storage ...... 298 B.4.1 Implementation Model ...... 298 B.4.2 AE Specifications ...... 298 B.4.2.1 OsiriX Media Exporter ...... 298 B.4.2.2 OsiriX Media Importer ...... 299 B.4.3 Augmented and Private Profiles ...... 299 B.5 Support for Extended Character Sets ...... 299

C Lexicon 301

Bibliography 305

Index 307