https://github.com/recoh/iliopsoas_muscle

Large-Scale Analysis of Iliopsoas Muscle Volumes in the UK Biobank
https://github.com/recoh/iliopsoas_muscle

Last synced: 2 days ago
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Large-Scale Analysis of Iliopsoas Muscle Volumes in the UK Biobank

• Host: GitHub
• URL: https://github.com/recoh/iliopsoas_muscle
• Owner: recoh
• License: mit
• Created: 2020-11-06T10:41:34.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2020-11-17T09:57:58.000Z (almost 4 years ago)
• Last Synced: 2024-08-02T16:46:07.181Z (3 months ago)
• Language: Jupyter Notebook
• Size: 167 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-uk-biobank - iliopsoas_muscle - scale analysis of iliopsoas muscle volumes in the UK Biobank | (Imaging phenotypes / Abdominal MRI)

README

        
# Large-Scale Analysis of Iliopsoas Muscle Volumes in the UK Biobank

If you use the code or the model in your work, please cite:

- Fitzpatrick J, Basty N, Cule M, Liu Y, Bell JD, Thomas EL, Whitcher B. Large-Scale Analysis of Iliopsoas Muscle Volumes in the UK Biobank, 2020, *Scientific Reports*, DOI: [10.1038/s41598-020-77351-0][scientific-reports].

## Installation

Execute `git-lfs checkout` in the directory containing the `git clone` output to download the deep learning models and example data.

```

# deactivate

# rm -rf ~/.venv/ipm

python3 -m venv ~/.venv/ipm 

source ~/.venv/ipm/bin/activate 

pip install --upgrade pip setuptools wheel 

cd ~/iliopsoas_muscle

pip install -r requirements.txt 

jupyter notebook 

```

Click on the link and then click on the `.ipynb` file to run the example in the browser.

## Pre-processing

The example subject from the UK Biobank was pre-processed using our [pipeline][pipeline] code.  

- Basty, N., Yiu, L., Cule, M., Thomas, E.L., Bell, J.D., Whitcher, B.  Image processing and quality control for 

abdominal magnetic resonance imaging in the UK Biobank, 2020, arXiv: [2007.01251][arxiv-pipeline].

[arxiv-ipm]: https://arxiv.org/abs/2008.05217

[arxiv-pipeline]: https://arxiv.org/abs/2007.01251

[pipeline]: https://github.com/recoh/pipeline

[scientific-reports]: https://dx.doi.org/10.1038/s41598-020-77351-0