Medical Image Test Data

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

Public Releases Private Releases

See this issue on Med-ImageTools for the discussion.

Development

Installation

pixi install

Usage

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

1. Check the "nbia_datasets.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

Access Type

This pipeline is by default, using the 'public' access type. The bhklab has a clone of this repo that runs the pipeline in private mode. To run the pipeline in private mode, you need to set up your environment variables:

export the username and password AND create a .env file with the credentials.

export NBIA_USERNAME=""
export NBIA_PASSWORD=""

Create a .env file like:

LOGIN__NBIA_USERNAME=""
LOGIN__NBIA_PASSWORD=""

You also need to set the ACCESS_TYPE to private

export ACCESS_TYPE=private

Running the pipeline

Then:

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.