CLI and YAML

YAML templates and habit commands live only here, not in the Habitat Guide. Copy a file from config/, edit the ★ fields (usually data and output paths), and run the matching command.

Command list: Command reference. Catalog of templates: Configuration recipe catalog.

• Configuration recipe catalog
  • By workflow
  • Starter demos
  • Field reference pages
• Habitat Segmentation Configuration
  • Habitat Analysis Configuration Parameters
• Feature Extraction Configuration
• Traditional Radiomics Configuration
  • paths
  • processing
  • export
  • logging
  • Backward-compatible flat keys
  • PyRadiomics parameter YAML
• Preprocessing Configuration
  • Preprocessing configuration parameters
  • DICOM sort configuration (habit sort-dicom)
• DICOM Sort Configuration
  • Top-level fields
  • Notes
• Auxiliary Tools and Data Configuration
  • Data configuration parameters
  • ICC analysis configuration (habit icc)
  • Traditional radiomics CLI configuration (habit radiomics)
  • Repository configuration template index
  • Configuration file validation
  • FAQ

Supporting bookmarks

These are not Habitat Guide pages. Templates live under config/.

• Image preprocessing (N4, resample, registration): Preprocessing Configuration

• DICOM sort / rename: DICOM Sort Configuration

• Dice, ICC, merge-csv, and other utilities: Auxiliary Tools and Data Configuration

• Whole-ROI radiomics CLI: Traditional Radiomics Configuration