Difference between revisions of "ITK-SNAP"

From UFRC
Jump to navigation Jump to search
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
+
[[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|itksnap}}
 
|{{#vardefine:app|itksnap}}
Line 29: Line 29:
 
*Extensive tutorials
 
*Extensive tutorials
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 80: Line 70:
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 19:23, 12 August 2022

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

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