Commit 4af93434 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Readme updates

parent 2ab0ed4f
...@@ -4,7 +4,9 @@ ...@@ -4,7 +4,9 @@
This repository contains Jupyter notebooks and data for the 2018 WIN PyTreat. This repository contains Jupyter notebooks and data for the 2018 WIN PyTreat.
The master repository can be found at: https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals The master repository can be found at:
https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals
To contribute to the practicals: To contribute to the practicals:
...@@ -14,3 +16,31 @@ To contribute to the practicals: ...@@ -14,3 +16,31 @@ To contribute to the practicals:
2. Make your changes on your fork 2. Make your changes on your fork
3. Submit a merge request back to the master repository 3. Submit a merge request back to the master repository
To run these notebooks in the `fslpython` environment, you must first install
jupyter:
```
source $FSLDIR/fslpython/bin/activate fslpython
conda install jupyter
pip install notedown
source deactivate
ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter
ln -s $FSLDIR/fslpython/envs/fslpython/bin/notedown $FSLDIR/bin/fslnotedown
```
> [`notedown`](https://github.com/aaren/notedown) is a handy tool which allows
> you to convert a markdownd (`.md`) file to a Jupyter notebook (`.ipynb`)
> file. So you can write your practical in your text editor of choice, and
> then convert it into a notebook, instead of writing the practical in the web
> browser interface.
Now you can start the notebook server from the repository root:
```
fsljupyter notebook
```
Supports Markdown
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