bastiencagna/deep_folding

Deep folding

The project aims to study cortical folding patterns thanks to deep learning tools. MRIs are processed through BrainVISA/Morphologist tools.

Prerequisites

Anatomist parts (anatomist_tools) must run with brainvisa installed and python2

Deep learning part (preprocessing and utils) must run with python3 and works with pytorch.

Package documentation can be found at https://neurospin.github.io/deep_folding/index.html.

Development

git clone https://github.com/neurospin/deep_folding.git

# Install for development
bv bash
cd deep_folding
virtualenv --python=python3 --system-site-packages venv
. venv/bin/activate
pip3 install -e .

# Tests
python3 -m pytest  # run tests

If you want to install the package:

python setup.py install

Notebooks are in the repertory notebooks, access using:

bv bash # to enter brainvisa environnment
. venv/bin/activate
jupyter notebook # then click on file to open a notebook

If you want to build the documentation and pushes it to the web:

bv bash # to enter brainvisa environnment
. venv/bin/activate
cd docs
./make_docs.sh

If you want to clean the documentation:

cd docs/source
make clean