CONTENTS

• TITLE PAGE
• 1. INTRODUCTION
• 2. CONCEPTS AND NOTATIONS
1. Window Objects
2. Input
• 3. GETTING STARTED
1. Main Menu
2. Image Formatter
3. Image Editor
4. Three-Dimensional Viewer
5. Dose Contours
6. Dose Plots
1. Dose-Depth Plotting
2. Dose-Volume Histogram Plotting
7. seraMC Interface
8. Dose Combination
9. Advanced Features
1. Launch Feature
2. Advanced Mode
3. Set Project Directory
4. Set Global Preferences
5. Closed Launched Applications
10. Help
• 4. IMAGE FORMATS
1. Image Formatting
2. File Menu
1. Load QSH Selection
2. Load Single Images Selection
3. Unload Images Selection
4. Generate Raw Images Selection
5. Save QSH Selection
6. Launch Selection
7. Check Version Selection
3. Options Menu
1. Edit QHD Selection
2. Tool Bar Selection
3. Messages Selection
4. Reverse Images Selection
5. Manipulate Images Selection
4. Preferences Menu
• 5. IMAGE EDITOR
1. File Menu
1. Open Selection
2. Save Selection
3. Launch Selection
4. Remove Bodies Selection
5. Restart Program Selection
6. Exit Program Selection
2. Edit Menu
1. Slice Information Selection
2. Relabel Regions Selection
3. Colormap Selection
4. Constraint Markers Selection
5. Fiducial Markers Selection
6. Sort Images by Z-Value Selection
7. Reverse Image Set Selection
3. View Menu
1. Properties Toolbar Selection
2. Edit Regions Selection
1. Setup Mode
2. Threshold Mode
3. Manual Draw Mode
4. Fill Mode
5. 3D Grow Mode
6. Copy Body Mode
7. Make Margin Mode
3. Context Help Selection
4. Bottom Information Selection
5. Cross-Section Tool Selection
6. Intensity Histogram Selection
7. Region Volumes Selection
4. Preferences Menu
5. Suggested Modeling Steps for BNCT Treatment Planning
1. Suggested Modeling Steps Using CT Image Sets
2. Suggested Modeling Steps Using MRI Image Sets
• 6. THREE-DIMENSIONAL RECONSTRUCTION
1. The Menubar
1. The File Menu
2. The Options Menu
3. The Preferences Menu
4. The Help Menu
2. The Message Bar
3. The Main Rendering Window
4. The Tools
1. Viewing Panel
2. Color Panel
3. Transparency Panel
4. Lighting Panel
5. Axes Panel
6. Clipping Panel
7. Polygon Panel
8. Particle Tracking Panel
9. Slice Panel
10. Contour Panel
11. Mouse Panel
12. View Parameters Panel
13. Beam Panel
14. Texture Mapping Panel
5. The Preferences
1. Window Sizes
2. Color
3. Axes
4. Mouse
5. Particle Paths
6. Texture
7. Miscellaneous
• 7. TRANSPORT MODELING
1. Introduction
2. Menus
1. Files Menu
2. Run Menu
3. Options Menu
3. Run Title Panel
4. Files Panel
1. Save Directory
2. CG Geom File Name
3. Patient Geom File Name
4. Old RST File Name
5. New RST File Name
6. Source File Name
7. Material File Name
8. Cross Section File Name
9. seraMC Run Script
10. Ultrafast Mode Files
5. Control Panel
1. Nbatch
2. Nhist
3. Run Directives
4. Run Date
6. Positioning Panel
1. Target Point Location
2. Distance to Target Point
3. Polar Angle
4. Azimuthal angle
7. Tally Panel
8. Auxilliary Panels
1. Beam Optimization and Automatic Positioning
2. Edit Isotopes
9. Edit Directives
10. Monitor Panel
• 8.  STATISTICAL DOSE COMBINATION
1. Introduction
2. Menus
1. File Menu
2. Edit Menu
3. Preferences Menu
1. Fields/Fractions Preferences
2. Reference Dose Preferences
3. Dose-volume Edit Options Preferences
4. Additional Dose-volume Edits Preferences
4. Help Menu
3. Combination Utility
1. Input data
1. Identification Parameters
1. Patient ID
2. Treatment Date
2. Field/Fraction Specifications
1. Number of Fractions
2. Number of Fields per Fraction
3. Set Button
3. Field Data
1. Dose File Name
2. Boron Concentration Data
3. Exposure Data
4. Gamma Repair Data
5. Active Field
2. Summation Data
1. Fraction Sum
2. Plan Sum
3. Output Files
1. Plan File
2. Combined Dose Files
4. Edit Module
1. Basic Input Data
1. Dose File
2. Plan Name
3. Patient ID
4. Blood B10
5. N_avg
6. Upper DV bin (%)
7. Nbin_DV
8. Reference Dose Search Component
9. Reference Dose Search Type
10. Reference Dose RBE Values
11. Perform Standard Edits Button
2. User-defined Edits Input Data
1. Point
2. Line
3. Dose-volume Histogram
4. Contour
3. Standard Edits
4. Output Files
1. Reference Dose
2. Point Edits
3. Line Edits
4. Dose-volume Histogram Edits
5. Contour Edits
1. Standard Edits
2. User-defined Edits
• 9. DOSE CONTOURING
1. File Menu
2. Color Menu
3. Options Menu
4. Help Menu
5. Loading Images
6. Loading Contours
7. Working with Contours
8. Loading Masks
9. Working with Masks
10. Working with Colors
11. Setting Preferences
12. Entering Dose Factors
13. Selecting Dose Components
14. Changing Field of View
15. The Image Contouring Window
• 10. 2D DOSE PLOTTING TOOLS
1. Introduction
2. Simplot
3. DVall
4. Patient Positioning
• 11. WORK IN PROGRESS
• 12. SYSTEM REQUIREMENTS
• 13. TROUBLESHOOTING
• 14. USER SUPPORT
• 15. REFERENCES
• APPENDIX A.  TRANSPORT CALCULATION MODULE (seraMC)
1. Introduction
2. General Problem Input
1. Line 1 - Title
2. Line 2 - Nbatch, nhist, wncut
3. Line 3 - Target Point
4. Line 4 - Zb, phi, theta
5. Line 5 - Combinatorial Geometry (CG) File
6. Line 6 - Univel File
7. Line 7 - Nedit2 and nnegp
8. Line 8 - Neutron energy group boundaries
9. Line 9 - X0, Y0, Z0
10. Line 10 - Delw
11. Line 11 - Old restart file
12. Line 12 - New restart file
13. Line 13 - Source file
14. Line 14 - Irand_num and ied
15. Line 15 - Run_dir and run_date
16. Line 16 - Material file
17. Line 17 - Cross section file
18. Line 18 - Edit isotopes
19. Line 19 - Run script for seraMC
20. Line 20 - Proton range file
21. Line 21 - Ultrafast directory file
22. Line 22 - Ultrafast cross section file
3. Coordinate Transformations
4. Automatic Beam Locator
1. Positioning when iop=1
2. Positioning when iop=2
3. Positioning when iop=3
4. Positioning when iop=4
5. Positioning when iop=5
5. Edit Directives
• APPENDIX B.  seraMC COMBINATORIAL GEOMETRY
1. Introduction
2. Body Input Specifications
1. Rectangular Parallelpiped (RPP)
2. Box (BOX)
3. Sphere (SPH)
4. Right Circular Cylinder (RCC)
5. Right Elliptical Cylinder (REC)
6. Truncated Right Angle Cone (TRC)
7. Ellipsoid (ELL)
8. Right Angle Wedge (WED)
9. Arbitrary Polyhedron of 4, 5, or 6 sides (ARB)
10. Right Vertical Wedge (RVW)
11. Restricted General Ellipsoid (RGE)
3. Combinatorial Geometry Descriptions
4. Examples of CG Descriptions
1. Example 1
2. Example 2
3. Example 3
4. Example 4
5. Example 5
5. Format of Combinatorial Geometry File
• APPENDIX C.  seraMC SOURCE DESCRIPTION
1. Introduction
2. Formats
3. Variable Descriptions
1. Nsorcs
2. Nmu
3. Xtnsn and Xtnsg
4. Dim
5. Fspec
6. Lreg, Mat, and Reg
• APPENDIX D.  seraMC EDIT DIRECTIVES
1. Introduction
2. Passive Directives
1. patient
2. date
3. beam
3. Reference Dose Parameters
1. refvol
2. refpoint
3. refdepth
4. ref_reg and more_ref
5. ref_b10
6. ref_rbe
4. General Parameters
1. mw_min
2. mw
3. b10_blood
4. b10_ratio
5. delta
6. eps
7. in_reg and more_reg
8. nbin_DV
9. rbe
10. images
11. ap, bp, and cp
12. skinentry
5. Active Edits
1. point
2. line
3. px, py, and pz
4. contour
5. ottocon
6. box
7. DVbs
8. fiducial
9. ras
10. beamplt
11. N_avg
12. crosshair
• APPENDIX E. seraConvert
1. Envoke seraConvert
2. Load Qsh and Spline Files
3. Making Sure all Bodies Are Known
4. Build the Univel Files
5. Varifying Results
6. Viewing Univel Files in SeraModel

Contact J. R. Venhuizen <jrv@inel.gov> with corrections and comments.