Installation¶

The project uses uv and Python ≥ 3.11. Runtime dependencies: pyxnat, dcm2bids, dcm2niix (the dcm2niix PyPI package vendors the binary onto your PATH), pydicom, cubids, nibabel (used to read NIfTI shapes for the mriconvert scans.tsv), pandas (used by bidsmap), and phys2bids (used by physioconvert to read physiological recordings and write BIDS physio files; see the note under xnatcli physioconvert about its numpy pin). bioread is also pulled in for phys2bids to read BIOPAC .acq files (phys2bids imports it lazily but does not depend on it directly).

uv sync
uv pip install -e .

The second command makes the xnatcli command available on your PATH inside the project's virtualenv. Activate the venv (source .venv/bin/activate on Unix, .venv\Scripts\activate on Windows) to use xnatcli directly, or invoke it with uv run xnatcli ….