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MLEBE

Build Status

MLEBE (Machine Learning Enabled Brain Extraction) is a python package for both the training of a 3D Unet for segmentation and its integration into the SAMRI workflow.

Installation

Python Package Manager (Users):

Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even). This approach cannot manage any of our numerous non-Python dependencies (by design) and at the moment will not even manage Python dependencies; as such, given any other alternative, we do not recommend this approach:

git clone https://github.com/Jimmy2027/MLEBE.git
cd MLEBE
python setup.py install --user

If you are getting a Permission denied (publickey) error upon trying to clone, you can either:

  • Add an SSH key to your GitHub account.
  • Pull via the HTTPS link git clone https://github.com/Jimmy2027/MLEBE.git.
Using a conda venv:
git clone https://github.com/Jimmy2027/MLEBE.git
cd MLEBE
path/to/conda/environment/bin/python -m pip install .

Python Package Manager (Developers):

Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even); it also allows you to install a "live" version of the package - dynamically linking back to the source code. This permits you to test code (with real module functionality) as you develop it. This method is sub-par for dependency management (see above notice), but - as a developer - you should be able to manually ensure that your package manager provides the needed packages.

git clone [email protected]:Jimmy2027/MLEBE.git
cd MLEBE
echo "export PATH=\$HOME/.local/bin/:\$PATH" >> ~/.bashrc
source ~/.bashrc
python setup.py develop --user

If you are getting a Permission denied (publickey) error upon trying to clone, you can either:

  • Add an SSH key to your GitHub account.
  • Pull via the HTTPS link git clone https://github.com/Jimmy2027/MLEBE.git.
Using a conda venv:
git clone https://github.com/Jimmy2027/MLEBE.git
cd MLEBE
path/to/conda/environment/bin/python -m pip install -e .

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