2014 Winter Project Week:Slicer CIP Modules

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Key Investigators

We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules, Python modules, and through a nipype work flow for their deployment in high performance computing environments.

The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
In the past few months, we have ported most of the available tools to CLIs
The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to develop a few python modules that execute a flow of commands using a sequence of CLIs in order to perform lung and lobe segmentation, and lung atlas to patient registration. The python modules should be available via both a graphical user interface and the command line. We also aim to define nipype interfaces that utilize the python modules for workflows that can be used for clinical purposes.

Private github repository: https://github.com/acil-bwh/SlicerCIP
Implemented a simple Python module that calls multiple CLIs in order to register a probabilistic lung atlas to a new patient CT volume