Documentation/Nightly/Modules/BrainExtractionTool - Revision history

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2016-11-26T01:02:02Z

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Acsenrafilho at 22:32, 25 November 2016

2016-11-25T22:32:24Z

Acsenrafilho at 18:11, 25 November 2016

2016-11-25T18:11:58Z

Acsenrafilho at 17:57, 25 November 2016

2016-11-25T17:57:50Z

Acsenrafilho at 23:55, 22 April 2016

2016-04-22T23:55:28Z

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2016-04-22T23:48:56Z

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2016-04-22T23:23:52Z

Acsenrafilho: Created page with "{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

← Older revision		Revision as of 12:46, 26 November 2016
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−	~~<noinclude>{{documentation/versioncheck}}</noinclude>~~
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−	~~{{documentation/{{documentation/version}}/module-header}}~~
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−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|Introduction and Acknowledgements}}~~
−	~~{{documentation/{{documentation/version}}/module-introduction-start\|{{documentation/modulename}} }}~~
−	~~{{documentation/{{documentation/version}}/module-introduction-row}}~~
−	This work was partially funded by CAPES and CNPq (grant 201871/2015-7/SWE), a Brazilian research support agency. Information on CAPES can be obtained from the official websites, [http://www.capes.gov.br/ CAPES here] and [http://www.cnpq.br/ CAPES here].<br>
−	~~Author: Antonio Carlos da S. Senra Filho, CSIM Laboratory (University of Sao Paulo, Department of Computing and Mathematics)<br>~~
−	~~Contact: Antonio Carlos da S. Senra Filho <email>acsenrafilho@usp.br</email><br>~~
−	~~{{documentation/{{documentation/version}}/module-introduction-row}}~~
−	~~{{documentation/{{documentation/version}}/module-introduction-logo-gallery~~
−	~~\|Image:CSIM-logo.png\|CSIM Laboratory~~
−	~~\|Image:USP-logo.png\|University of Sao Paulo~~
−	~~\|Image:CNPq-logo.png\|CNPq Brazil~~
−	~~\|Image:CAPES-logo.png\|CAPES Brazil~~
−	}}
−	~~{{documentation/{{documentation/version}}/module-introduction-end}}~~
−
−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|Module Description}}~~
−	~~{{documentation/{{documentation/version}}/module-description}}~~
−	~~[[Image:BrainExtractionTool-logo.png\|left]]~~
−	This module aims to extracted the brain in structural MRI images, namely T1 weighted MRI images. The method is based on the non-parametric algorithm proposed by Iglesias et. al. <ref> Iglesias, J.E. et al., 2011. "Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods". IEEE Transactions on Medical Imaging, 30(9), pp.1617–1634</ref>. The application with T2 and proton density MRI images were not intensively tested, but it is assumed that the algorithm is robust with those image contrasts as well. For more details about the brain extraction method, please check the [http://doi.org/10.1109/TMI.2011.2138152 original paper]
−
−	In addition, for better brain volume extraction results it could be applied some preprocessing steps such as a noise attenuation and field inhomogeneity correction methods in advance. See the modules [[Documentation/{{documentation/version}}/Modules/AADImageFilter\|AAD Image Filter]] and [[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection\|N4 Bias Field Correction]].
−
−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|Use Cases}}~~
−	~~Most frequently used for these scenarios:~~
−	* Use Case 1: Initial image processing step for many neuroimage analysis, such as in DTI and cortical thickness estimation.
−	**It would be useful for tissue classication.
−	* Use Case 2: Information reduction to registration pipelines
−	**The non-brain tissues tend to decrease the quality of many registration algorithms.
−	* Use Case 3: Increase the precision of classification algorithms for neurodegenerative brain diseases diagnosis.
−	**Could offer a better segmentation and classification on specific brain image analysis such as in Multiple Sclerosis lesion segmentation as well as the global brain atrophy.
−
−	~~<gallery>~~
−	~~Image:AllHeadMRI.png\|T1w MRI~~
−	~~Image:BrainMRI.png\|Brain extracted T1 MRI~~
−	~~</gallery>~~
−
−
−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|Tutorials}}~~
−	~~N/A~~
−
−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|Panels and their use}}~~
−	~~[[Image:BrainExtractionTool-GUI.png\|thumb\|380px\|User Interface]]~~
−	*Input Volume:
−	**Insert an input scalar volume
−	*Output Volume:
−	**Set the output volume
−
−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|Similar Modules}}~~
−	*[[Documentation/{{documentation/version}}/Modules/SkullStripper\|Skull Stripper]]
−	*[[Documentation/{{documentation/version}}/Modules/SwissSkullStripper\|Swiss Skull Stripper]]
−
−	~~<!-- ---------------------------- -->~~
−	~~{{documentation/{{documentation/version}}/module-section\|References}}~~
−	* [http://dcm.ffclrp.usp.br/csim Computing in Signals and Images in Medicine Laboratory (CSIM)]
−
−	~~Repositories:~~
−	* Source code: [https://github.com/CSIM-Toolkits/BrainExtractionTool GitHub repository]
−	* Issue tracker: [https://github.com/CSIM-Toolkits/BrainExtractionTool/issues open issues and enhancement requests]
−
−
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−	~~{{documentation/{{documentation/version}}/module-footer}}~~
−	~~[[Category:Documentation/{{documentation/version}}/Modules/Informatics]]~~
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@@ Line 50: / Line 50: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
-[[Image:brainextractiontool_gui.png|thumb|380px|User Interface]]
+[[Image:BrainExtractionTool-GUI.png|thumb|380px|User Interface]]
 *Input Volume:
 **Insert an input scalar volume

@@ Line 55: / Line 55: @@
 *Output Volume:
 **Set the output volume
 <!-- ---------------------------- -->

@@ Line 24: / Line 24: @@
 {{documentation/{{documentation/version}}/module-description}}
 [[Image:BrainExtractionTool-logo.png|left]]
-This module aims to extracted the brain in structural MRI images, namely T1 weighted MRI images. The method is based on the non-parametric algorithm proposed by Iglesias et. al. <ref> Iglesias, J.E. et al., 2011. "Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods". IEEE Transactions on Medical Imaging, 30(9), pp.1617–1634</ref>. The application with T2 and proton density MRI images were not intensively tested, but it is assumed that the algorithm is robust with those image contrasts as well.
+This module aims to extracted the brain in structural MRI images, namely T1 weighted MRI images. The method is based on the non-parametric algorithm proposed by Iglesias et. al. <ref> Iglesias, J.E. et al., 2011. "Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods". IEEE Transactions on Medical Imaging, 30(9), pp.1617–1634</ref>. The application with T2 and proton density MRI images were not intensively tested, but it is assumed that the algorithm is robust with those image contrasts as well. For more details about the brain extraction method, please check the [http://doi.org/10.1109/TMI.2011.2138152 original paper]
 In addition, for better brain volume extraction results it could be applied some preprocessing steps such as a noise attenuation and field inhomogeneity correction methods in advance. See the modules [[Documentation/{{documentation/version}}/Modules/AADImageFilter|AAD Image Filter]] and [[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection|N4 Bias Field Correction]].
@@ Line 68: / Line 68: @@
 Repositories:
-* Source code: [https://github.com/CSIM-Toolkits/Slicer GitHub repository]
+* Source code: [https://github.com/CSIM-Toolkits/BrainExtractionTool GitHub repository]
-* Issue tracker:  [https://github.com/CSIM-Toolkits/Slicer/issues open issues and enhancement requests]
+* Issue tracker:  [https://github.com/CSIM-Toolkits/BrainExtractionTool/issues open issues and enhancement requests]

@@ Line 23: / Line 23: @@
 {{documentation/{{documentation/version}}/module-section|Module Description}}
 {{documentation/{{documentation/version}}/module-description}}
+[[Image:BrainExtractionTool-logo.png|left]]
 This module aims to extracted the brain in structural MRI images, namely T1 weighted MRI images. The method is based on the non-parametric algorithm proposed by Iglesias et. al. <ref> Iglesias, J.E. et al., 2011. "Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods". IEEE Transactions on Medical Imaging, 30(9), pp.1617–1634</ref>. The application with T2 and proton density MRI images were not intensively tested, but it is assumed that the algorithm is robust with those image contrasts as well.

← Older revision		Revision as of 23:55, 22 April 2016
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	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-section\|Panels and their use}}		{{documentation/{{documentation/version}}/module-section\|Panels and their use}}
		+	[[Image:brainextractiontool_gui.png\|thumb\|380px\|User Interface]]
		+	*Input Volume:
		+	**Insert an input scalar volume
		+	*Output Volume:
		+	**Set the output volume
		+	*Binary Mask:
		+	**Set the output binary mask, i.e. the label generated by the brain given in the output volume.

−	~~\|[[Image:brainextractiontool_gui.png\|thumb\|380px\|User Interface]]~~

@@ Line 41: / Line 41: @@
 <gallery>
 Image:AllHeadMRI.png|T1w MRI
 Image:BrainMRI.png|Brain extracted T1 MRI
 </gallery>
@@ Line 58: / Line 58: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
-*[[https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SkullStripper|Skull Stripper]]
+*[[Documentation/{{documentation/version}}/Modules/SkullStripper|Skull Stripper]]
-*[[https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SwissSkullStripper|Swiss Skull Stripper]]
+*[[Documentation/{{documentation/version}}/Modules/SwissSkullStripper|Swiss Skull Stripper]]
 <!-- ---------------------------- -->