DBP:Harvard:Software:Testing:EMABC Validation - Revision history

Dougm at 18:05, 10 January 2007

2007-01-10T18:05:57Z

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 # Atlas Registration: Warping a template atlas to the case being segmented which yields four probability atlases (one for every tissue class, one for background). Currently this is performed by a Python script written by Alexandre Guimond.
 # EM Segmentation: The expectation maximization procedure separates MR data into background, face, CSF, gray matter, and white matter. Up to now this is accomplished by a Tcl script written by Kilian Pohl.
 ===1.3. New pipeline: The EMAtlasBrainClassifier module in Slicer:===

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 Katharina Quintus, PNL <i>{ kquintus -at- bwh.harvard.edu }</i>
-==Introduction==
+==1. Introduction==
 ===1.1 Goals:===

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 ===1.3. New pipeline: The EMAtlasBrainClassifier module in Slicer:===
-[[Image:EMABC-1.jpg|250px|right|Figure 1: The EMAtlasBrainClassifier Module user interface in Slicer
+[[Image:EMABC-1.jpg|250px|right|Figure 1: The EMAtlasBrainClassifier Module user interface in Slicer]]
 The EMAtlasBrainClassifier module basically implements the same expectation maximization algorithm as the Tcl script used in the current PNL processing pipeline. However, this module performs all four processing steps with a single button press. The user has to define the structural volume and the corresponding T2 volume and decides if step one (coregistration) is needed or not. Furthermore the user can turn on/off the output of various intermediate results of the segmentation algorithm under  ”Advanced Tab”.  Figure 1 shows a screenshot of the user interface of the EMAtlasBrainClassifier Module in Slicer.

@@ Line 21: / Line 21: @@
 ===1.3. New pipeline: The EMAtlasBrainClassifier module in Slicer:===
 The EMAtlasBrainClassifier module basically implements the same expectation maximization algorithm as the Tcl script used in the current PNL processing pipeline. However, this module performs all four processing steps with a single button press. The user has to define the structural volume and the corresponding T2 volume and decides if step one (coregistration) is needed or not. Furthermore the user can turn on/off the output of various intermediate results of the segmentation algorithm under  ”Advanced Tab”.  Figure 1 shows a screenshot of the user interface of the EMAtlasBrainClassifier Module in Slicer.
 An important feature is the possibility to toggle multi threading. Segmentation results were found to be dependent on the number of CPUs. This is due to the parallel implementation of the segmentation algorithm. To guarantee comparable results between computers with different numbers of CPUs, multithreading will be turned off in our new processing pipeline.

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 =Validating Slicer Module 'EMAtlasBrainClassifier'=
-Katharina Quintus, PNL
+Katharina Quintus, PNL <i>{ kquintus -at- bwh.harvard.edu }</i>
 ==Introduction==

← Older revision		Revision as of 17:59, 10 January 2007
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	[[Image:EMABC-fig11.jpg\|frame\|center\|\|Figure 11: Jaccard measure, outliers labeled]]		[[Image:EMABC-fig11.jpg\|frame\|center\|\|Figure 11: Jaccard measure, outliers labeled]]

		+	[[Image:EMABC-fig12.jpg\|frame\|center\|\|Figure 12: Volume difference measure, outliers removed]]
		+
		+	[[Image:EMABC-fig13.jpg\|frame\|center\|\|Figure 13: Jaccard measure, outliers removed]]

	===2.4 Conclusion===		===2.4 Conclusion===

← Older revision		Revision as of 17:54, 10 January 2007
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	[[Image:EMABC-fig9.jpg\|frame\|center\|\|Figure 9: CSF volume, outliers labeled.]]		[[Image:EMABC-fig9.jpg\|frame\|center\|\|Figure 9: CSF volume, outliers labeled.]]
		+
		+	[[Image:EMABC-fig10.jpg\|frame\|center\|\|Figure 10: Volume difference measure, outliers labeled]]
		+
		+	[[Image:EMABC-fig11.jpg\|frame\|center\|\|Figure 11: Jaccard measure, outliers labeled]]

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-[[Image:EMABC-fig7.jpg|frame|center||Figure 7: White matter volume, with outliers labeled.
+[[Image:EMABC-fig7.jpg|frame|center||Figure 7: White matter volume, with outliers labeled.]]
-[[Image:EMABC-fig8.jpg|frame|center||Figure 8: Gray matter volume, outliers labeled.
+[[Image:EMABC-fig8.jpg|frame|center||Figure 8: Gray matter volume, outliers labeled.]]
-[[Image:EMABC-fig9.jpg|frame|center||Figure 9: CSF volume, outliers labeled.
+[[Image:EMABC-fig9.jpg|frame|center||Figure 9: CSF volume, outliers labeled.]]

← Older revision		Revision as of 17:32, 10 January 2007
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−	~~PLOTS~~	+	[[Image:EMABC-fig7.jpg\|frame\|center\|\|Figure 7: White matter volume, with outliers labeled.
		+
		+	[[Image:EMABC-fig8.jpg\|frame\|center\|\|Figure 8: Gray matter volume, outliers labeled.
		+
		+	[[Image:EMABC-fig9.jpg\|frame\|center\|\|Figure 9: CSF volume, outliers labeled.

← Older revision		Revision as of 17:22, 10 January 2007
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−	~~SCATTERPLOT~~	+	[[Image:EMABC-fig6.jpg\|frame\|center\|\|Figure 6: The Jaccard measure]]
		+

	: There are some cases where the Jaccard measure indicates that the segmentations do not overlap well. We had a closer look at those outliers.		: There are some cases where the Jaccard measure indicates that the segmentations do not overlap well. We had a closer look at those outliers.