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.

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 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.