Installation

Installation

Requirements

• Python 3.11+
• PyRadiomics, SimpleITK, lifelines, scikit-learn, statsmodels, scipy, pandas — pulled in automatically as dependencies.

Install

pip install -e .            # core CLI + library
pip install -e .[rtstruct]  # plus rt-utils for `qr convert rtstruct`

After install, three equivalent entry points are on $PATH — qr, qradiomics, qrdx — all pointing at qradiomics.cli.main:cli.

Verify:

qr --version
qr info

Kick-off script (clone + install + smoke test)

curl -sSL https://raw.githubusercontent.com/choilab-jefferson/qradiomics/main/scripts/kickoff.sh | bash

scripts/kickoff.sh clones the repo (if needed), creates a .venv, runs pip install -e ., runs qr info, and runs the smoke tests. Environment knobs:

Variable	Purpose
QR_REPO_URL / QR_REPO_DIR	override clone source / target
QR_BRANCH	branch to check out
QR_PYTHON	python interpreter
QR_VENV	venv path (set to - to skip the venv)
QR_SKIP_SMOKE=1	skip the pytest smoke run

Smoke test (no data download)

python3 -m pytest tests/ -q          # analyze + results.merge (19 tests)
python3 scripts/smoke.py             # 5-patient synthetic NRRD chain, no TCIA needed

Next

• Quick Start — end-to-end TCIA example
• CLI Reference — full command list