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Welcome to the ChestImagingPlatform

The ChestImagingPlatform (CIP) is open-source library for image-based phenotyping of Chest CT images. This toolkit is developed at Brigham and Women's Hospital under funding for the NIH NHLBI.

#Building Instructions In order to build CIP you will need to set up your environment with the following prerequisites

##Prerequisites

*CMake > 2.8.9: CIP uses CMake for cross-platform building *Git > 1.7.10: Distributed version control system. CIP is hosted in GitHub. Additional dependencies will be retrieved using git tools *SVN > 1.7: Subversion control system *Anaconda = 2.1: Anaconda is the python distribution used by CIP to handle the python dependencies. ###Installation notes about Anaconda The simplest way is to perform a full installation of the Anaconda distribution. If you prefer a more lightweight approach, you can install the Miniconda package. This is a barebone python with the conda installer. Make sure that you update your Anaconda distribution with the following packages that are used by CIP by launching a terminal and running:

conda install pip numpy scipy cython scikit-learn vtk
pip install nipype pynrrd pydicom

Building CIP

Launch a terminal and execute

git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatform-build
ccmake ../ChestImagingPlatform

CMake will give you the options to set-up different configuration options. Make sure that the SuperBuild option is marked if you want CIP to install and compile all the dependencies for you. Then run configure and generate on cmake. After that all you have to do is to build CIP

make -j 2