Documentation/4.3/Modules/LASegmenter - Revision history

Liangjiazhu at 05:23, 1 November 2013

2013-11-01T05:23:36Z

Liangjiazhu at 04:12, 29 October 2013

2013-10-29T04:12:03Z

Liangjiazhu at 02:36, 29 October 2013

2013-10-29T02:36:33Z

Liangjiazhu at 02:36, 29 October 2013

2013-10-29T02:36:12Z

Liangjiazhu at 02:28, 29 October 2013

2013-10-29T02:28:52Z

UpdateBot: Nightly -> 4.3

2013-09-05T03:43:14Z

Nightly -> 4.3

New page

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 

Contributor: LiangJia Zhu, University of Alabama at Birmingham 
Contributor: Yi Gao, Brigham and Women's Hospital 
Contributor: Josh Cates, University of Utah 
Contributor: Alan Morris, University of Utah 
Contributor: Danny Perry, University of Utah 
Contributor: Greg Gardner, University of Utah 
Contributor: Rob MacLeod, University Utah 
Contributor: Allen Tannenbaum, University of Alabama at Birmingham 
Contact: LiangJia Zhu, <email>ljzhu@uab.edu</email> 
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{{documentation/{{documentation/version}}/module-section|Module Description}}
This module performs the segmentation of the left atrium from MR images. It is an implementation of a region-growing-based method with a shape prior. The module starts from a manually generated seed region inside the left atrium. Then, the growing process gradually captures the whole left atrium region.



{{documentation/{{documentation/version}}/module-section|Use Cases}}
This module is specifically designed for the segmentation of the left atrium from MR images.


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*Load source image [[file:LASegLoad.png]]
 

*Selct Editor module
# Choose Master Volume and Merge Volume (label map to be used for the left atrium seed region)
# Select PaintEffect and adjust Radius (in mm) so that the painted seed region (a circle) is completetly inside the left atrium
# Go to the Axial view, choose a slice that is approximately to the center of the left atrium. Then, draw a circle that lies to the center of the left atrium on the slice
[[file:LASegSeedPanel.png|350px]][[file:LASegSeedImage.png]]

 
*Go to Segmentation->Left Atrium Segmentation module
# Select Original Image, Seed Label Image (the one obtained from the Editor module), and select/create Segmentation Results
# Adjust parameters if needed
# Press Apply button and it takes several mimutes to process one volume
[[file:LASegPanel.png|350px]][[file:LASegResult.png]]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
NA


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Extensions/CardiacMRIToolkit|CARMA]]


{{documentation/{{documentation/version}}/module-section|References}}
L. Zhu, Y. Gao, A. Yezzi, R. MacLeod, J. Cates, A. Tannenbaum. Automatic Segmentation of the Left Atrium from MRI Images Using Salient Feature and Contour Evolution, IEEE Engineering in Medicine and Biology Conference(EMBC), 2012.


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@@ Line 10: / Line 10: @@
 This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
-Contributor: Liangjia Zhu, University of Alabama at Birmingham <br>
+Contributor: Liangjia Zhu, Stony Brook University <br>
-Contributor: Yi Gao, Brigham and Women's Hospital<br>
+Contributor: Yi Gao, University of Alabama at Birmingham <br>
 Contributor: Josh Cates, University of Utah <br>
 Contributor: Alan Morris, University of Utah <br>
@@ Line 17: / Line 17: @@
 Contributor: Greg Gardner, University of Utah <br>
 Contributor: Rob MacLeod, University Utah <br>
-Contributor: Allen Tannenbaum, University of Alabama at Birmingham <br>
+Contributor: Allen Tannenbaum, Stony Brook University <br>
-Contact: Liangjia Zhu, <email>ljzhu@uab.edu</email><br>
+Contact: Liangjia Zhu, <email>liangjia.zhu@stonybrook.edu</email><br>
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@@ Line 18: / Line 18: @@
 Contributor: Rob MacLeod, University Utah <br>
 Contributor: Allen Tannenbaum, University of Alabama at Birmingham <br>
-Contact: LiangJia Zhu, <email>ljzhu@uab.edu</email><br>
+Contact: Liangjia Zhu, <email>ljzhu@uab.edu</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}
 {{documentation/{{documentation/version}}/module-introduction-logo-gallery

@@ Line 10: / Line 10: @@
 This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
-Contributor: LiangJia Zhu, University of Alabama at Birmingham <br>
+Contributor: Liangjia Zhu, University of Alabama at Birmingham <br>
 Contributor: Yi Gao, Brigham and Women's Hospital<br>
 Contributor: Josh Cates, University of Utah <br>

@@ Line 17: / Line 17: @@
 Contributor: Greg Gardner, University of Utah <br>
 Contributor: Rob MacLeod, University Utah <br>
-Contributor: Allen Tannenbaum, Stony Brook University <br>
+Contributor: Allen Tannenbaum,  Stony Brook University <br>
 Contact: Liangjia Zhu, <email>liangjia.zhu@stonybrook.edu</email><br>
 {{documentation/{{documentation/version}}/module-introduction-row}}
@@ Line 50: / Line 50: @@
 *Select Editor module
 # Choose Master Volume and Merge Volume (label map to be used for the left atrium seed region)
-# Select PaintEffect and adjust Radius (in mm) so that the painted seed region (a circle) is completetly inside the left atrium
+# Select PaintEffect and adjust Radius (in mm) so that the painted seed region (a circle) is completely inside the left atrium
 # Go to the Axial view, choose a slice that is approximately to the center of the left atrium. Then, draw a circle that lies to the center of the left atrium on the slice
 [[file:LASegSeedPanel.png|350px]][[file:LASegSeedImage.png]]
@@ Line 58: / Line 58: @@
 # Select Original Image, Seed Label Image (the one obtained from the Editor module), and select/create Segmentation Results
 # Adjust parameters if needed
-# Press Apply button and it takes several mimutes to process one volume
+# Press Apply button and it takes several minutes to process one volume
 [[file:LASegPanel.png|350px]][[file:LASegResult.png]]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
-NA
+A properly set seed region is required to start the segmentation process. In principle, the seed region needs to be set closely to the center of the left atrium and covers the most of left atrium region on the selected image slice. The radius of a seed region is determined by the size of the left atrium. A small radius may cause the segmentation terminates before reaching the left atrium boundary. A large radius may lead to oversegmentation. Examples of good seed regions with various radius from small to large are shown below:
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