ITK-SNAP
Description
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.
Citation
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.
doi:10.1016/j.neuroimage.2006.01.015