installation.md

Direct Installation

Part of this repository contains a Python package called body_comp, which should be installed before running any of the code. Once you have cloned this repository you can install the body_comp package and all its dependencies by running this command from the root of the repository:

$ pip install .

Note that this will not install the gdcm python package, because it is not in the PyPI package repository. Having this package installed is important to be able to decompress some of the less common DICOM transfer syntaxes (compression methods). If you are using Anaconda, you can install the gdcm package from their repositories. On a Mac, you can install gdcm with:

brew install gdcm --with-python3

Alternatively, you can get the gdcm package by directly downloading a release from the github repository or installing from source (see the Dockerfile for an example of this process). Note that you must have not just the C++ library, but also the Python bindings for Python 3 installed.