Deep folding

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

Prerequisites

Brainvisa parts (deep_folding.brainvisa) must run with brainvisa installed (see steps below)

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

Generates datasets of crops

Deep learning pipelines to investigate folding patterns are not working on the whole brain (or the whole hemisphere) but on brain crops. Several processings are required, as drawn here:

We give a step-by-step description of the pipeline in deep_folding/brainvisa/README.rst.

The pixi way (recommended)

First install aims, anatomist and morphologist library:

# First install pixi (no need to be root) if it is not installed
curl -fsSL https://pixi.sh/install.sh | bash
source ~/.bashrc

# Create the pixi environment

mkdir env_pixi
cd env_pixi
pixi init -c conda-forge -c https://brainvisa.info/neuro-forge
pixi add anatomist soma-env=0.0 morphologist pip ipykernel

Then, activate the pixi shell and install deep_folding:

pixi shell
# Install deep_folding
git clone https://github.com/neurospin/deep_folding.git
cd deep_folding
SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True pip3 install -e .

# Launch the tests to check the installation
python3 -m pytest

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
# To avoid the scikit-learn naming error use
SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True pip3 install -e .
# instead of
# pip3 install -e .

# Tests
python3 -m pytest  # run tests

If you want to install the package:

python3 setup.py install

Notebooks are in the folder 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
pip3 install -e .[doc]
cd docs
./make_docs.sh

If you want to clean the documentation:

cd docs/source
make clean