Documentation/4.0/Modules/EMSegment Easy - Revision history

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:33:00Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

JChris.FillionR at 10:20, 2 February 2012

2012-02-02T10:20:44Z

Pohl at 02:07, 10 December 2011

2011-12-10T02:07:55Z

Pohl: /* Step 5: Define Miscellaneous Parameters */

2011-11-23T20:04:42Z

Step 5: Define Miscellaneous Parameters

Pohl: /* Step 3: Specify Intensity Distribution */

2011-11-23T20:02:59Z

Step 3: Specify Intensity Distribution

Pohl: /* Step 2: Define Anatomical Tree */

2011-11-23T19:59:44Z

Step 2: Define Anatomical Tree

Pohl: /* Step 1: Define Input Datasets */

2011-11-23T19:57:42Z

Step 1: Define Input Datasets

Pohl: /* Step 1: Define Input Channel */

2011-11-23T19:57:14Z

Step 1: Define Input Channel

Pohl at 19:52, 23 November 2011

2011-11-23T19:52:22Z

Pohl at 19:51, 23 November 2011

2011-11-23T19:51:43Z

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 *Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

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 === 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 ===
+=== Step 5: Miscellaneous ===
-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.
+This panels allows the user to specify the region of interest to be segmented. Pressing the 'Segment' button starts the segmentation.
 Once the parameters are specified, the target images are segmented
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-Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section
+Please visit the [[ Documentation/4.0#Segmentation | segmentation section ]] for similar modules
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 The user specifies the number of structures to be segmented and the label of each structure. You can further add class to an existing structure by right-clicking on the structure and selecting "Add sub-class". The label and corresponding color of a structure are modified by selecting the structure in the tree.
-=== Step 3: Specify Intensity Distribution ===
+=== Step 3: Sampling and Class Weights ===
-Defining the intensity distribution for each structure of interest through taking samples in the image of interest
+Define the intensity distribution for each structure of interest by taking samples in the image of interest. Users can also specify the relative to weight of a node in the tree with respect to other structures. If a class should be overestimated in the final label map then this can be adjusted by lowering the weight of that structure and repeating the segmentation.
 === 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

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 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  ===
+=== Step 2: Define Structure  ===
-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.
+The user specifies the number of structures to be segmented and the label of each structure. You can further add class to an existing structure by right-clicking on the structure and selecting "Add sub-class". The label and corresponding color of a structure are modified by selecting the structure in the tree.
 === Step 3: Specify Intensity Distribution ===
 Defining the intensity distribution for each structure of interest through taking samples in the image of interest

@@ Line 36: / Line 36: @@
 === 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. If using multiple modes which are not aligned with each other then check on the check-box button "Align input scans".
+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  ===

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-Most frequently used for these scenarios:
+MR image segmentation
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-Links to tutorials that use this module
+N/A
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-A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:
+=== Step 1: Define Input Channel  ===
-{|style="width: 100%"
+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.
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 * Point to other modules that have similar functionality
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 {{documentation/{{documentation/version}}/module-section|References}}
-Publications related to this module go here. Links to pdfs would be useful.
+* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.
-For extensions: link to the source code repository and additional documentation
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