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".
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
.
- Simply install
repo2docker
from pyPI:
pip install jupyter-repo2docker
- 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:https://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:
- Run
docker images
command and copy theIMAGE ID
to your clipboard - 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:
This repository is created by Notebok-Factory.