Modules:EMSegment-Simple-3.4
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Module Name
EM Segment Simple
General Information
Module Type & Category
Type: CLI
Category: Segmentation
Authors, Collaborators & Contact
- Brad Davis: Kitware, Inc.
- Kilian Pohl: IBM
- Sebastien Barre: Kitware, Inc.
- Yumin Yuan: Kitware, Inc.
- Polina Golland: MIT
- Contact: Brad Davis, brad.davis@kitware.com
Module Description
This module provide a simplified "one-click" GUI interface for the EMSegment Command-line Executable. The interface is simple because the number of required command-line parameters is minimized, and it is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.
Usage
Similar to the EMSegment Command-line Executable, once a set of parameters for segmentation algorithm is deemed satisfactory through the process of calibrating in the Template Builder module, the user will commonly want to bypass this detailed calibration process when segmenting new images. This module provides a simple interface to specify a small number of required command-line parameters --- a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image --- , and to allow any EM algorithm parameters to be modified, within the MRML scene, via the EMSegment GUI interface.
Examples, Use Cases & Tutorials
- 2008 Tutorial
These slides and data describe the Slicer3 implementation of the EMSegmenter and demonstrate its use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.
Quick Tour of Features and Use
- Parameters panel:
- MRML Scene: Select the tutorial parameter set
- Result Labelmap: Select a new image filename
- Target Volumes: Select input target volumes from one of the target directories (e.g., Target_NewPatient1)
Note: target volume order is important
- Click `Apply’, wait (~30 minutes for full size images)…
Development
The overall design of the EMSegmenter module is described in these slides.
The module is implemented as a programmatic Slicer3 module because it requires a large degree of interaction with the user, the data stored in the MRML tree, and the Slicer3 GUI itself. Because the MRML node structure is rather complicated (for example the anatomical tissue hierarchy and a large number of interdependent nodes) the Logic class is solely responsible for maintaining and accessing these nodes. The Logic class provides an API that the GUI code uses to access and modify data. The Logic class also wraps the algorithm code itself.
Dependencies
Slicer3 base modules.
Known bugs
Follow this link to the Slicer3 bug tracker.
Usability issues
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
- 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.
Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.
Source code & documentation
Links for the module.
More Information
For more information about the EM Segmenter project in Slicer3 see the old EMSegment Wiki page here The old EMSegmenter FAQ contains frequently asked questions about the EMSegment interfaces in Slicer3. There is also an old EMSegmenter Mini-Tutorials
Acknowledgment
Funding for the EMSegmenter module was provided by NAMIC.
References
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. A Hierarchical Algorithm for MR Brain Image Parcellation. IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [bib]
