Medical Image Test Data

This repository aims to source medical images for BHKLAB radiomics test data.

Releases

See this issue on Med-ImageTools for the discussion.

Ideally, the results of this pipeline should be version controlled and set up as release artifacts on GitHub.

Development

Installation

pixi install

Usage

This project is just a snakemake pipeline that does the following:

1. Check the "nbia.yaml" for the list of collectiond
2. Create a job for each collection that then checks the nbia.yaml for the list of patients
   1. For each patient, get ALL the series
   2. Download all the series into a 'rawdata' directory
3. tar.gz each collection in the 'rawdata' directory into the procdata directory

pixi run snake

Release

Upon a new tag being generated on github, the pipeline will be run and the results will be packaged into a release artifact. See Releases for all the releases.