Prepare data

Project root

Run commands from the project root (folder containing config/ ):

Portable pack: extract directory (same level as python.exe )
Source: GitHub repo root

Paths in YAML are resolved relative to the YAML file location unless absolute.

Folder layout

data_root/
├── images/
│   └── subject001/
│       ├── T1/T1.nii.gz
│       └── T2/T2.nii.gz
└── masks/
    └── subject001/
        ├── T1/mask.nii.gz
        └── T2/mask.nii.gz

See demo_data/preprocessed/processed_images/ after extracting the demo.

Data specification

Folder: data_dir points to a root with images/ and masks/
Manifest YAML (recommended): data_dir points to e.g. config/habitat/file_habitat_demo.yaml

Draw ROIs in ITK-SNAP or 3D Slicer ; export NIfTI masks.

Templates: config/ — see Configuration recipe catalog.