https://github.com/bhklab/med-image_test-data
https://github.com/bhklab/med-image_test-data
Last synced: 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/bhklab/med-image_test-data
- Owner: bhklab
- License: other
- Created: 2025-01-16T15:47:42.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2025-02-14T16:28:39.000Z (4 months ago)
- Last Synced: 2025-02-14T16:35:03.470Z (4 months ago)
- Language: Python
- Homepage:
- Size: 1.06 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Medical Image Test Data
This repository aims to source medical images for BHKLAB
radiomics test data.
[Releases](https://github.com/bhklab/med-image_test-data/releases)
See [this issue on Med-ImageTools](https://github.com/bhklab/med-imagetools/issues/173)
for the discussion.
Ideally, the results of this pipeline should be version controlled
and set up as release artifacts on GitHub.
## Development
### Installation
```bash
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
Create a `.env` file like:
```
LOGIN__NBIA_USERNAME=""
LOGIN__NBIA_PASSWORD=""
```
Then:
```bash
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](https://github.com/bhklab/med-image_test-data/releases) for all the releases.