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_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

Validation

Validated 4/5/2018

ITK-SNAP