2013 Summer Project Week:Nipype CLI Integration

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Home < 2013 Summer Project Week:Nipype CLI Integration

Key Investigators

  • BWH: Rola Harmouche,Demian Wassermann, Raul San Jose (BWH)


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 and through a nipype work flow for their deployment in high performance computing environments.

Approach, Plan

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 port most of these tools to the CLI infrastructure and to define nipype interfaces.


  • The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
  • This week we decided to deliver the tools through several extensions consisting of python modules. Each module executes a flow of commands by calling CLIs
  • We completed the CLIs for 1 of the extensions (as an example), and are working on the scripted module


Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a

Slicer Module Extension -- commandline


  • James C. Ross, R. San Jose Estepar, G. Kindlmann, Alejandro Diaz, C.-F. Westin, Edwin K. Silverman, George R. Washko, [Automatic Lung Lobe Segmentation Using Particles, Thin Plate Splines, and Maximum a Posteriori Estimation] Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010 Volume 6363, Pages 163-171, 2010
  • Gordon Kindlmann, Raúl San José Estépar, Stephen M. Smith, Carl-Fredrik Westin. Sampling and Visualizing Creases with Scale-Space Particles. IEEE Transactions on Visualization and Computer Graphics. 2009; 15(6):1415-1424.
  • San José Estépar, R. et al., 2012. Computational Vascular Morphometry for the Assessment of Pulmonary Vascular Disease based on Scale-Space Particles. In Proceedings of the 9th IEEE International Symposium on Biomedical Imaging (ISBI) 2012. Barcelona, pp. 1479–1482.