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Installing from source (on *nix)

  1. Clone project: git clone https://github.com/freesurfer/samseg.git

  2. Get the submodules: git submodule init git submodule update

  3. Create a virtual environment using, e.g., conda: conda create -n samseg python=3.9

  4. Activate the virtual environment: conda activate samseg

  5. Install requirements: python -m pip install -r requirements.txt

  6. Install correct compilers for ITK v.4.13.2 conda install -c conda-forge gxx_linux-64=7.5 gcc_linux-64=7.5 sysroot_linux-64=2.17

  7. Create the ITK build directory mkdir ITK-build cd ITK-build

  8. Export compilers installed with conda: export CC=<your_conda_path>/envs/samseg/bin/x86_64-conda_cos6-linux-gnu-gcc export CC=<your_conda_path>/envs/samseg/bin/x86_64-conda_cos6-linux-gnu-g++

  9. Run CMAKE: cmake \ (samseg) -DBUILD_SHARED_LIBS=OFF \ -DBUILD_TESTING=OFF \ -DBUILD_EXAMPLES=OFF \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX=../ITK-install \ ../ITK

  10. Install: make install

  11. Build python wheel (or create and editable install using develop instead of bdist_wheel) ITK_DIR=ITK-install python setup.py bdist_wheel