View source for ITK-SNAP

[[Category:Software]][[Category:Bioinformatics]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|itksnap}}
|{{#vardefine:url|http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.HomePage}}
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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
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==Required Modules==
===Serial===
* {{#var:app}}
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===Parallel (OpenMP)===
* intel
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===Parallel (MPI)===
* intel
* openmpi
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==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==

ITK-SNAP is a GUI application and can be used only on [[GUI Programs|GUI server]] for short-term lightweight operations.
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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (Licensing, usage, access).
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{{#if: {{#var: testing}}|==Performance==
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} 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. 

[http://doi:10.1016/j.neuroimage.2006.01.015 doi:10.1016/j.neuroimage.2006.01.015]
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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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=Validation=
* Validated 4/5/2018