Readme updates

README.md

@@ -4,7 +4,9 @@
 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:
@@ -14,3 +16,31 @@ To contribute to the practicals:
 2. Make your changes on your fork
 
 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
+```