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The quest for measuring myelin with MRI - An interactive meta-analysis

Matteo Mancini, Agah Karakuzu, Thomas Nichols, Julien Cohen-Adad, Mara Cercignani, Nikola Stikov


This repository generates the interactive figures and the meta-analysis results for our study "The quest for measuring myelin with MRI – An interactive meta-analysis of quantitative comparisons with histology".

📎The full preprint is available on bioRxiv.

🖥 Usage instructions

This Jupyter Book is published by NeuroLibre at https://neurolibre.github.io/myelin-meta-analysis, where all the interactive content is made readily available!

However, several options are available if you would like to reproduce the outputs by re-executing the code.

💻 Execute locally

The required packages can be installed using pip:

pip install -r requirements.txt

Note:

R and the metafor package are both needed to fit the mixed-effect model in meta-analysis.ipynb through the package rpy2. Alternatively, you can use the conda environment described in environment.yml.

🐳 Use with Docker

If you have Docker installed on your computer and running, you can run the code in the same environment described in this repository using repo2docker.

  1. Simply install repo2docker from pyPI:
pip install jupyter-repo2docker
  1. Run the following command in your terminal:
jupyter-repo2docker https://github.com/neurolibre/myelin-meta-analysis

After building (it might take a while!), it should output in your terminal something like:

Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://0.0.0.0:36511/?token=f94f8fabb92e22f5bfab116c382b4707fc2cade56ad1ace0

This should start a Jupyter session on your browser and make all the resources you see when you launch a Binder for this repository.

To re-use your container built by repo2docker, do the following:

  1. Run docker images command and copy the IMAGE ID to your clipboard
  2. Run the following command to start the container:
docker run -it --rm -p 8888:8888 `PASTE IMAGE ID HERE` jupyter notebook --ip 0.0.0.0
☁️ Zero installation

You can use Interact Inline or Launch in Binder buttons at the top of each page of the Jupyter Book.

Alternatively, you can start a Binder session by clicking the badge below:

Binder



This repository is created by Notebok-Factory.