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Reorder README
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mathieuboudreau authored Feb 14, 2024
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Expand Up @@ -12,6 +12,14 @@ Click on the badge "Open in Colab" ☝️. The notebook takes about 2 hours to r

## Run in a Docker container (NeuroLibre, MyBinder, repo2ocker)

### repo2docker

To run locally on your computer, you must first have Docker installed, running, and have created an account. Follow the instructions [here](https://www.docker.com/get-started/).

Then, you need to install [repo2docker](https://github.com/jupyterhub/repo2docker). Install via pip: `pip install jupyter-repo2docker`

To launch a Docker session from this repo, run `repo2docker --ref main https://www.github.com/shimming-toolbox/rf-shimming-7t`. After it's completed, it will provie you with a weblink, copy and open this link in a browser to open the Jupyter Notebook session.

### NeuroLibre

> [!NOTE]
Expand All @@ -27,14 +35,6 @@ Click on the badge "launch binder" ☝️. This environment setup downloads the

If you'd like to re-run the processing from scratch, change the `notebook = 'neurolibre-figures'` line in the first cell to `notebook = 'neurolibre-clean'`. This will delete the processed files and then re-run the entire processing pipeline. Note that some cells take a lot of RAM, and may fail on certain systems.

### repo2docker

To run locally on your computer, you must first have Docker installed, running, and have created an account. Follow the instructions [here](https://www.docker.com/get-started/).

Then, you need to install [repo2docker](https://github.com/jupyterhub/repo2docker). Install via pip: `pip install jupyter-repo2docker`

To launch a Docker session from this repo, run `repo2docker --ref main https://www.github.com/shimming-toolbox/rf-shimming-7t`. After it's completed, it will provie you with a weblink, copy and open this link in a browser to open the Jupyter Notebook session.

## Run locally with Jupyter Notebook

Install [Spinal Cord Toolbox](https://spinalcordtoolbox.com/user_section/installation.html)
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