ITK-SNAP

Description

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

Required Modules

Serial

• itksnap

System Variables

• HPC_{{#uppercase:itksnap}}_DIR

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