https://github.com/agahkarakuzu/myelin-meta-analysis

Code for the bioRxiv preprint "The quest for measuring myelin with MRI – An interactive meta-analysis of quantitative comparisons with histology"

https://github.com/agahkarakuzu/myelin-meta-analysis

Repository

Code for the bioRxiv preprint "The quest for measuring myelin with MRI – An interactive meta-analysis of quantitative comparisons with histology"

https://github.com/agahkarakuzu/myelin-meta-analysis/blob/master/

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.](https://www.biorxiv.org/content/10.1101/2020.07.13.200972v2)



##  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
```
2. 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](https://mybinder.org/v2/gh/neurolibre/myelin-meta-analysis/master) 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](https://github.com/zelenkastiot/binder_badges/blob/master/badges/myelin--meta--analysis-binder.svg)](https://mybinder.org/v2/gh/neurolibre/myelin-meta-analysis/master)








 

This repository is created by Notebok-Factory. 

Owner

GitHub Events

Issues and Pull Requests

Last synced: 10 months ago