README.md

2018 WIN PyTreat

This repository contains Jupyter notebooks and data for the 2018 WIN PyTreat.

The upstream repository can be found at:

https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals

To contribute to the practicals:

1. Fork the upstream repository on gitlab

2. Make a local clone of your fork:

   git clone git@git.fmrib.ox.ac.uk:<username>/pytreat-2018-practicals

3. Add the upstream repository as a remote:

   git remote add upstream git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git

4. Make your changes on your local repository

5. Rebase onto the upstream repository, and push your changes to your fork:

   git fetch --all
   git rebase upstream/master
   git push --force origin master

6. In gitlab, submit a merge request from your fork back to the upstream repository.

To run these notebooks in the fslpython environment, you must first install jupyter:

# If your FSL installation requires administrative privileges to modify, then
# you MUST run these commands as root - don't just prefix each individual
# command with sudo, or you will probably install jupyter into the wrong
# location!
#
# One further complication - once you have become root, $FSLDIR may not be set,
# so either set it as we have ione below, or make sure that it is set, before
# proceeding.
sudo su
export FSLDIR=/usr/local/fsl
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 is a handy tool which allows you to convert a markdown (.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. If you install notedown as suggested in the code block above, you can run it on a markdown file like so:

fslnotedown my_markdown_file.md > my_notebook.ipynb

Now you can start the notebook server from the repository root:

fsljupyter notebook