CLI Commands API

Command Line Interface

HABIT provides a command-line interface through the habit command.

Main Commands

habit preprocess       # Preprocess images
habit sort-dicom       # DICOM rename/sort only (dcm2niix -r y)
habit get-habitat      # Habitat segmentation (train / predict)
habit extract          # Extract habitat features
habit model            # Train or predict ML models (--mode train|predict)
habit cv               # K-fold cross-validation
habit compare          # Model comparison plots and DeLong test
habit radiomics        # Traditional radiomics (standalone)
habit icc              # ICC analysis
habit retest           # Test-retest reproducibility
habit dice             # Dice between two mask batches
habit dicom-info       # Inspect DICOM metadata
habit merge-csv        # Merge CSV/Excel files by index column
habit gui              # Web GUI (under development)

For detailed CLI documentation, see the command help:

habit --help
habit get-habitat --help