FAQ

Install

``habit`` not found — you are not in the conda env. On Windows open Anaconda Prompt (not plain CMD), run conda activate habit until the prompt shows (habit), then habit --version. See Installation.

``pip install`` fails / mirror missing package — use official PyPI:

pip install habitat-analysis -i https://pypi.org/simple

PyRadiomics on Windows — do not use bare pip install pyradiomics (broken sdist). Install the wheel from Release v1.0.2 matching your Python, e.g. 3.10:

pip install https://github.com/lichao312214129/HABIT/releases/download/v1.0.2/pyradiomics-3.1.0-cp310-cp310-win_amd64.whl

napari / ``PluginManifest`` / pydantic errors:

pip install "pydantic>=2.12,<3"
pip install "napari[pyqt5]" "npe2>=0.8.2" "pydantic!=2.11.*,>=2.8,<3" -i https://pypi.org/simple

napari window flashes then closes — keep show=True (default); the call blocks until you close the window.

``OptionalDependencyError`` — the message includes the pip install ... command for the missing package.

Parquet / pyarrow — pip install pyarrow, or set habitats_results_format: csv in YAML.

Run

Path / file errors — run from the project root (folder that contains config/). Check data_dir / out_dir (and absolute paths if unsure).

Command failed — habit <cmd> --help; read processing.log in the output folder; validate with habit check-config -c <yaml>.

YAML changes ignored — confirm the file passed with -c; CLI --mode overrides YAML run_mode.

Data

ROI: NIfTI aligned with images, or resample the mask (Load from NIfTI files). Directory, loose files, SimpleITK, or NumPy: 1. Data In. DICOM: Preprocessing.

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