2018 WIN PyTreat

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

• The talks directory contains some (but not all) of the Topyc talks that will be given throughout the week.

• The getting_started directory contains a series of practicals intended for those of you who are new to the Python programming language, or need a refresher.

• The advanced_topics directory contains a series of practicals on various aspects of the Python programming language - these are intended for those of you who are familiar with the basics of Python, and want to learn more about the language.

The practicals have been written under the assumption that FSL 5.0.10 is installed.

For attendees

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 done 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
source deactivate
ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter

Then, clone this repository on your local machine, and run fsljupyter notebook:

git clone git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git
cd pytreat-2018-practicals
fsljupyter notebook

Throughout the week we might make changes to this repository. When this happens, we will ask you to update your local clone of the repository with the following command:

git reset --hard HEAD
git pull origin master

Note that this will overwrite any changes that you have made to the files in your repository!

Have fun!

For contributors

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.

When you install jupyter above, you may also wish to install notedown:

# .
# see instructions above
# .
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