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| − | [[Documentation|Return to Slicer Documentation]]
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| − | __NOTOC__
| + | http://www.slicer.org/slicerWiki/index.php/Modules:EM-Segmenter-Documentation-3.2 . |
| − | ===Module Name===
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| − | MyModule
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| − | {|
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| − | |[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]
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| − | |[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]
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| − | |[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
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| − | |}
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| − | | |
| − | == General Information ==
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| − | ===Module Type & Category===
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| − | Type: Interactive (Template Builder) and CLI (EMSegment Simple)
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| − | Category: Segmentation
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| − | ===Authors, Collaborators & Contact===
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| − | * Kilian Pohl: Harvard
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| − | * Brad Davis: Kitware, Inc.
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| − | * Sebastien Barre: Kitware, Inc.
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| − | * Yumin Yuan: Kitware, Inc.
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| − | * Polina Golland: MIT
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| − | * Contact: Brad Davis, brad.davis@kitware.com
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| − | ===Module Description===
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| − | The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.
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| − | As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.
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| − | == Usage ==
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| − | ===Examples, Use Cases & Tutorials===
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| − | * Note use cases for which this module is especially appropriate, and/or link to examples.
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| − | * Link to examples of the module's use
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| − | * Link to any existing tutorials
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| − | | |
| − | ===Quick Tour of Features and Use===
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| − | List all the panels in your interface, their features, what they mean, and how to use them. For instance:
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| − | * '''Input panel:'''
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| − | * '''Parameters panel:'''
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| − | * '''Output panel:'''
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| − | * '''Viewing panel:'''
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| − | == Development ==
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| − | The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides]]
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| − | | |
| − | ===Dependencies===
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| − | Slicer base modules.
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| − | ===Known bugs===
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| − | Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
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| − | | |
| − | ===Usability issues===
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| − | The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
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| − | *Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.
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| − | Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.
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| − | ===Source code & documentation===
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| − | Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.
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| − | *[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
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| − | *API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]
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| − | == More Information ==
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| − | For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
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| − | ===Acknowledgment===
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| − | Funding for the EMSegmenter module was provided by NAMIC.
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| − | ===References===
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| − | K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.
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| − | [http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]
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