Introduction¶

Welcome to an interactive MRI course! This online course is divided in 4 chapters (for more info see 📕 Course chapters ) that demonstrate different MRI techniques and display the results in Jupyer notebooks. The notebooks are written in Julia (1.4.1) and Python (3.7).

If you are curious on how to use this Jupyter-book interface, download the codes or reproduce the figures see these sections:

📕 Course chapters

1: Sensitivity encoded MRI reconstruction

Preview: https://nbviewer.jupyter.org/github/nankueichen/education_SENSE_MRI/blob/main/main.ipynb
Complete files: https://github.com/nankueichen/education_SENSE_MRI

2: Magnitude and phase data processing for multi-TE gradient-echo MRI

Preview: https://nbviewer.jupyter.org/github/nankueichen/multi_TE_MRI/blob/main/main.ipynb
Complete files: https://github.com/nankueichen/multi_TE_MRI

3: DTI data processing

Preview: https://nbviewer.jupyter.org/github/nankueichen/education_DTI_processing/blob/main/main.ipynb
Complete files: https://github.com/nankueichen/education_DTI_processing

4: RF pulse design:

Preview: https://nbviewer.jupyter.org/github/sequintoa/BME639-RF/blob/master/Lab/RFPulse.ipynb
Complete files: https://github.com/sequintoa/BME639-RF/tree/master/Lab

🐳 Docker enviroment

Dockerfile for running a Docker image able to run SoS Jupyter notebooks (Julia: 1.4.1, Python: 3.7)

Run Docker locally

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://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 the IMAGE 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

☁️ Run on the cloud

You can use Live Code 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:

MRI online course

Introduction¶