Difference between revisions of "ITK-SNAP"

Latest revision as of 19:23, 12 August 2022

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

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Imaging]]
+[[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|itksnap}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 29: / Line 29: @@
 *Extensive tutorials
 <!--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==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 49: / Line 39: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+ITK-SNAP is a GUI application and can be used only on [[GUI Programs|GUI server]] for short-term lightweight operations.
 |}}
 <!--PBS scripts-->