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- Registration
  - General Registration (BRAINS)
  - Landmark Registration
  - Metric Test
  - Resample Image
  - Resize Image
  - Transforms
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    - Fiducial Registration
    - Reformat
    - Vector Demon Registration (BRAINS)
- Segmentation
  - Editor
  - EMSegmenter with Atlas
  - EMSegmenter without Atlas
  - Segment Editor
  - Simple Region Growing Segmentation
  - Specialized
    - EMSegment Command-line
    - Foreground masking (BRAINS)
    - Robust Statistics Segmenter
- Quantification
  - DataProbe
  - Label Statistics
  - Label Statistics (BRAINS)
  - PET Standard Uptake Value Computation
- Diffusion
  - TODO
- IGT
  - TODO
- Filtering
  - TODO
- Surface Models
  - TODO
- Converters
  - TODO
- Endoscopy
  - TODO
- Utilities
  - TODO
- Developer Tools
  - TODO
- Legacy
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- Testing
  - TODO
- Filter
  - TODO
- Multi-volume support
  - TODO
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