Table of Contents
- 1. Introduction
- 2. Basics
- 3. Help
- 4. Interface and User Actions
- 5. Toolbar
- 6. Open
- 7. DICOM Operations and De-identification
- 8. Save
- 9. View
- 10. Grayscale Window
- 11. Layers
- 12. Draw Raster ROIs
- 13. ROI
- 13.1. Morphology (group)
- 13.2. Remove “Salt and Pepper” artefacts
- 13.3. Union Cylinder from 2D Contours
- 13.4. Band of Average Signal
- 13.5. Intersect Cylinder from 2D Contours
- 13.6. Fill 2D Contours
- 13.7. Extract Atlas ROIs
- 13.8. Threshold to ROI by Signal interval
- 13.9. Threshold to ROI by Signal-to-Gradient ratio
- 13.10. Local Otsu Threshold to ROI
- 13.11. Split ROI with Threshold (group)
- 13.12. Normalize by ROI
- 13.13. Make Convex 2D
- 13.14. Clip Volume by ROI
- 13.15. Crop Volume by ROI
- 13.16. Clear ROI slices (group)
- 13.17. Average ROI layers
- 13.18. Convert 3D to 4D
- 13.19. Max Connected Component 3D
- 13.20. Max Connected Component 2D
- 13.21. Connected Component by Seed
- 13.22. Inside Surface Wave distance (in 0.01 mm)
- 13.23. Outside Surface Wave distance (in 0.01 mm)
- 13.24. Layer Peel
- 13.25. Smooth Shape
- 13.26. Volumetric profile curve
- 13.27. Concentric layers first order statistics
- 13.28. Zoom whole extent
- 14. Vector
- 14.1. Display VROIs
- 14.2. Construct VROI
- 14.3. Matching VROI coordinates to voxel indices
- 14.4. Activate, resize and move a VROI
- 14.5. Vector ROI properties
- 14.6. List all VROIs
- 14.7. Save VROIs
- 14.8. Load VROIs
- 14.9. Next VROI (F11)
- 14.10. Enclose connected components by a Vector ROI
- 14.11. Vector ROI 2D > 3D
- 14.12. Rasterize
- 14.13. Insert polyline
- 14.14. Delete
- 15. Volume
- 15.1. Window Center/Width setting
- 15.2. Advance to (timepoint)
- 15.3. Crop
- 15.4. Pad
- 15.5. Noise
- 15.6. Smooth over (optional) ROI
- 15.7. Smooth across Dynamic dimension
- 15.8. Volume Edge-constrained Smooth
- 15.9. Inter-Volume Edge-Constrained Smooth
- 15.10. Non-local Means Denoising
- 15.11. Texture Edge Detector with optional Constraint ROI
- 15.12. 3D Edge Detector
- 15.13. Single Scale Texture Gradient
- 15.14. Multiscale Texture Gradient
- 15.15. Multiscale Texture Gradient with 4D Aggregate
- 15.16. Depth to Time
- 15.17. Time to Depth
- 15.18. Copy voxels from current timepoint to target timepoint
- 15.19. Adaptive Threshold
- 15.20. Convert 2D Mosaic to Volume
- 15.21. Volume type conversion
- 15.22. Voxel Value Conversion
- 15.23. Insert Uniform Layer
- 15.24. Set DICOM tags
- 15.25. Set Volume Orientation
- 15.26. Change Patient Position and Orientation
- 16. Texture Edge Detection
- 17. Texture Analysis
- 18. Trace
- 19. Transform
- 19.1. Rotate and Create new volume (changes voxel size)
- 19.2. Rotate Orthogonal and Create new volume (preserves voxel size)
- 19.3. Load landmark file
- 19.4. Landmark alignment to a single Z-slice
- 19.5. Transform using VTF file
- 19.6. Save Alignment (*.vtf)
- 19.7. Make isotropic
- 19.8. Mirror voxels along axis (X, Y, Z)
- 19.9. Translate Active layer using vector
- 19.10. Rotate Active layer using sector
- 19.11. Discard Alignment
- 19.12. Active layer: Project to single slice volume
- 20. Nonuniformity
- 20.1. Introduction to MRI nonuniformity correction
- 20.2. Nonuniformity correction methods in FireVoxel
- 20.3. N3 and N4 algorithms
- 20.4. N3 (NYU implementation)
- 20.5. N4 (UPenn implementation)
- 20.6. N4 Explorer
- 20.7. BiCal algorithm
- 20.8. BiCal nonuniformity correction
- 20.9. BiCal Explorer
- 20.10. Measure {CV, CJV, Spillover} for two ROI layers
- 20.11. Measure {CJV, Spillover} for two ROI layers (All Documents)
- 21. Coregister with DICOM Tags
- 22. Coregister with AutoFocus
- 23. Coregister with Landmarks
- 24. Segmentation 3D: EdgeWave
- 25. Segmentation 4D
- 26. CT Abdominal Segmentation
- 26.1. Load and display images
- 26.2. Segment Whole Fat Mask (current slice)
- 26.3. Produce Subcutaneous and Visceral Fat Masks
- 26.4. Segment Abdominal fat using Abdominal Cavity ROI (current slice)
- 26.5. Measure VAT/(SAT+VAT) ratio (current slice)
- 26.6. Single Slice 2D: Segment SAT, VAT, MAT and Muscle using Abdominal Cavity contour (MagTrace)
- 26.7. Measure SAT, VAT, MAT and Muscle
- 27. Dynamic Analysis
- 28. Calculate Parametric Map
- 29. Models
- 30. Diffusion-Weighted MRI (DWI)
- 31. IVIM
- 32. T2 and T2* Mapping
- 33. Basics of DCE MRI
- 34. MRI Signal to Concentration
- 35. DCE MRI Model Analysis
- 36. Image-Derived Input Function
- 37. Cardiac Output Measurement and Correction
- 38. White Matter Lesion Segmentation on FLAIR MRI
- 39. Radiomics 2D Features