Multi-center benchmarking of cervical spinal cord RF coils at 7 T: A traveling spines study

This repository contains a reproducible Jupyter notebook for the manuscript titled "Multi-center benchmarking of cervical spinal cord RF coils at 7 T: A traveling spines study"

See the notebook results

You can access the processed notebooks with outputs by clicking on the Jupyter Book badge 👆

Run the notebook locally

Pre-requesites

• (recommended) Linux or MacOS
• A virtual environment with Python 3.10.x installed
  • e.g. Using a miniforge installation, conda create -n coil-qc python=3.10 in a terminal then follow instructions for activation.
• Version 6.5 of the Spinal Cord Toolbox (SCT)
  • git clone --depth 1 --single-branch --branch 6.5 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git
  • Follow the SCT Installation instructions for your operating system.

Installation

Clone the latest release of this repository, eg. for release r20250319:

git clone --depth 1 --single-branch --branch r20250319 https://github.com/spinal-cord-7t/coil-qc-code.git 
cd coil-qc-code

Install Python dependencies for the dowloaded version (ensure that the virtual environment is created, see pre-requesites section above)

pip install -r requirements-freeze.txt

Note: If you downloaded a non-release version of this repository, or if the command above doesn't work for you, run pip install -r requirements.txt to download the latest releases of the dependencies.

Run the notebooks

jupyter notebook data_processing-human.ipynb
jupyter notebook data_processing-phantom.ipynb

Alternatively, you can execute the notebooks by building a Jupyter Book with jupyter-book build .:

jupyter-book build .

and then open the resulting ./_build/html/index.html file in your web browser.