Documentation/4.0/Modules/EMSegment Easy
Introduction and Acknowledgements
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This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the NAC website. | |||||
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Module Description
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail:
Use Cases
MR image segmentation
Tutorials
N/A
Panels and their use
Step 1: Define Input Datasets
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes.
Step 2: Define Anatomical Tree
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.
Step 3: Specify Intensity Distribution
Defining the intensity distribution for each structure of interest through taking samples in the image of interest
Step 4: Edit Node-based Parameters
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step
Step 5: Define Miscellaneous Parameters
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.
Once the parameters are specified, the target images are segmented using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm.
Similar Modules
Please look at Segmentation section
References
- Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. Adaptive segmentation of MRI data. IEEE Trans Med Imaging. 1996; 15(4):429-442.
- Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. A Bayesian model for joint segmentation and registration. Neuroimage. 2006 May 15;31(1):228-39.
- 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]
Information for Developers
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Section under construction. |
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