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itksnap website  

SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, SNAP provides a number of supporting utilities. Some of the core advantages of SNAP include

  • Linked cursor for seamless 3D navigation
  • Manual segmentation in three orthogonal planes at once
  • Friendly UI for selecting active contour segmentation parameters
  • Support for many different 3D image formats, including NIfTI
  • Support for concurrent, linked viewing and segmentation of multiple images
  • Limited support for color images (e.g., diffusion tensor maps)
  • 3D cut-plane tool for fast post-processing of segmentation results
  • Extensive tutorials

Environment Modules

Run module spider itksnap to find out what environment modules are available for this application.

System Variables

  • HPC_ITKSNAP_DIR - installation directory

Additional Information

ITK-SNAP is a GUI application and can be used only on GUI server for short-term lightweight operations.


If you publish research that uses itksnap you have to cite it as follows:

Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage. 2006 Jul 1; 31(3):1116-28.