Algorithm:UNC:Shape Analysis - Revision history

Styner: /* Software */

2015-03-06T22:08:08Z

Software

Styner: /* Current status */

2015-03-06T22:07:17Z

Current status

Styner at 15:17, 11 May 2010

2010-05-11T15:17:16Z

Styner: /* Current status */

2009-05-05T01:56:18Z

Current status

Styner: /* Current status */

2009-05-05T01:55:55Z

Current status

Styner: /* Slicer integration */

2009-05-05T01:55:24Z

Slicer integration

Styner: /* Slicer integration */

2007-04-24T03:04:25Z

Slicer integration

Styner at 02:53, 24 April 2007

2007-04-24T02:53:13Z

Styner: /* Correspondence */

2007-04-24T02:51:02Z

Correspondence

Styner: /* Correspondence */

2007-04-24T02:50:47Z

Correspondence

@@ Line 46: / Line 46: @@
 == Software ==
-* SPHARM-PDM based framework for '''shape''' '''analysis''' [http://www.ia.unc.edu/dev/download/shapeAnalysis Binary Download], also available via [http://www.ia.unc.edu/dev/tutorials/Developer/index.htm CVS open source access]
+* SPHARM-PDM based framework for '''shape''' '''analysis''' is also available via [http://www.nitrc.org/projects/spharm-pdm/CVS NITRC]
 == Publications ==

@@ Line 39: / Line 39: @@
 === Current status ===
 In order to add the UNC shape analysis tools to the current 3D Slicer distribution do the following:
-# Download the distribution from http://www.ia.unc.edu/dev/download/shapeAnalysis/ (only linux 32 and 64 bit)
+# Download Slicer (e.g. version 4.4.0)
-# Copy all the executables to a folder with Slicer plugins or add the executable folder to the module path in Slicer (View->Application Settings->Module Settings)
+# Start the extension manager and download the SPHARM-PDM and ShapePopulationViewer extensions
-# start Slicer
+# restart Slicer
 # all individual steps can be run now without problem (they are listed under the Shape Analysis category)
 == Software ==

← Older revision		Revision as of 15:17, 11 May 2010
Line 1:		Line 1:
		+	This page is an older summary version of the pages linked at the [[ Algorithm:UNC \| UNC algorithms page]] and the [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM \| SPHARM PDM framework page]].
		+
	== Description ==		== Description ==

@@ Line 37: / Line 37: @@
 === Current status ===
 In order to add the UNC shape analysis tools to the current 3D Slicer distribution do the following:
-#) Download the distribution from http://www.ia.unc.edu/dev/download/shapeAnalysis/ (only linux 32 and 64 bit)
+# Download the distribution from http://www.ia.unc.edu/dev/download/shapeAnalysis/ (only linux 32 and 64 bit)
-#) Copy all the executables to a folder with Slicer plugins or add the executable folder to the module path in Slicer (View->Application Settings->Module Settings)
+# Copy all the executables to a folder with Slicer plugins or add the executable folder to the module path in Slicer (View->Application Settings->Module Settings)
-#) start Slicer
+# start Slicer
-#) all individual steps can be run now without problem (they are listed under the Shape Analysis category)
+# all individual steps can be run now without problem (they are listed under the Shape Analysis category)
-#) in order to run the comprehensive ShapeAnalysis tool (which is the recommended way to do this), one needs to run the following thing:
+# in order to run the comprehensive ShapeAnalysis tool (which is the recommended way to do this), one needs to run the following thing:
   Slicer3 --exec KWShapeAnalysisTool
 This last step is a current work around, which will be corrected this summer. While one can see the KWShapeAnalysis module (under the UNC category), it will not work unless started as described above.

@@ Line 37: / Line 37: @@
 === Current status ===
 In order to add the UNC shape analysis tools to the current 3D Slicer distribution do the following:
-a) Download the distribution from http://www.ia.unc.edu/dev/download/shapeAnalysis/ (only linux 32 and 64 bit)
+#) Download the distribution from http://www.ia.unc.edu/dev/download/shapeAnalysis/ (only linux 32 and 64 bit)
-b) Copy all the executables to a folder with Slicer plugins or add the executable folder to the module path in Slicer (View->Application Settings->Module Settings)
+#) Copy all the executables to a folder with Slicer plugins or add the executable folder to the module path in Slicer (View->Application Settings->Module Settings)
-d) start Slicer
+#) start Slicer
-e) all individual steps can be run now without problem (they are listed under the Shape Analysis category)
+#) all individual steps can be run now without problem (they are listed under the Shape Analysis category)
-f) in order to run the comprehensive ShapeAnalysis tool (which is the recommended way to do this), one needs to run the following thing:
+#) in order to run the comprehensive ShapeAnalysis tool (which is the recommended way to do this), one needs to run the following thing:
-Slicer3 --exec KWShapeAnalysisTool
+ Slicer3 --exec KWShapeAnalysisTool
 This last step is a current work around, which will be corrected this summer. While one can see the KWShapeAnalysis module (under the UNC category), it will not work unless started as described above.

← Older revision		Revision as of 01:55, 5 May 2009
Line 34:		Line 34:

	The individual shape analysis components have also been integrated into Slicer 3 modules. While it is entirely possible to run all steps of our shape analysis pipeline by calling the individual modules, this is highly inefficient. As a result we are developing, and a first prototype is ready, a separate shape pipeline tool to called from within Slicer3. This tool creates pipeline scripts for Batchmake, another NAMIC supported project at Kitware, to run the shape analysis pipeline as a distributed, background process. The whole shape analysis pipeline thus becomes entirely encapsulated and accessible to the trained clinical collaborator.		The individual shape analysis components have also been integrated into Slicer 3 modules. While it is entirely possible to run all steps of our shape analysis pipeline by calling the individual modules, this is highly inefficient. As a result we are developing, and a first prototype is ready, a separate shape pipeline tool to called from within Slicer3. This tool creates pipeline scripts for Batchmake, another NAMIC supported project at Kitware, to run the shape analysis pipeline as a distributed, background process. The whole shape analysis pipeline thus becomes entirely encapsulated and accessible to the trained clinical collaborator.
		+
		+	=== Current status ===
		+	In order to add the UNC shape analysis tools to the current 3D Slicer distribution do the following:
		+	a) Download the distribution from http://www.ia.unc.edu/dev/download/shapeAnalysis/ (only linux 32 and 64 bit)
		+	b) Copy all the executables to a folder with Slicer plugins or add the executable folder to the module path in Slicer (View->Application Settings->Module Settings)
		+	d) start Slicer
		+	e) all individual steps can be run now without problem (they are listed under the Shape Analysis category)
		+	f) in order to run the comprehensive ShapeAnalysis tool (which is the recommended way to do this), one needs to run the following thing:
		+	Slicer3 --exec KWShapeAnalysisTool
		+	This last step is a current work around, which will be corrected this summer. While one can see the KWShapeAnalysis module (under the UNC category), it will not work unless started as described above.

	== Software ==		== Software ==

← Older revision		Revision as of 03:04, 24 April 2007
Line 31:		Line 31:
	== Slicer integration ==		== Slicer integration ==

		+	A considerable amount of work was spent on the development aspect of our shape analysis tools. The main visualization tool, KWMeshVisu, can be called directly from Slicer 3 for the overlay of scalar, vector and ellipsoid data onto surfaces (so-called attribution) and the application of a set of versatile colormaps. The display of a saved "attributed" surfaces is then again possible within Slicer 3 to close the loop. This lean visualization tool fills a niche and is also used in our cortical thickness analysis tool.
		+
		+	The individual shape analysis components have also been integrated into Slicer 3 modules. While it is entirely possible to run all steps of our shape analysis pipeline by calling the individual modules, this is highly inefficient. As a result we are developing, and a first prototype is ready, a separate shape pipeline tool to called from within Slicer3. This tool creates pipeline scripts for Batchmake, another NAMIC supported project at Kitware, to run the shape analysis pipeline as a distributed, background process. The whole shape analysis pipeline thus becomes entirely encapsulated and accessible to the trained clinical collaborator.

	== Software ==		== Software ==

@@ Line 28: / Line 28: @@
 Current development is extending the framework to include subject variables, such as gender, age and clinical scores into the current pure group difference computation.
 == Publications ==
@@ Line 48: / Line 56: @@
 * G. Gerig, K. Muller, E. Kistner, Y. Chi, M. Chakos, M. Styner, J. Lieberman: Age and treatment related local hippocampal changes in schizophrenia explained by a novel '''shape''' '''analysis''' method, Medical Image Computing and Computer-Assisted Intervention MICCAI 2003, II, pp. 651-660.
 * M. Styner, G. Gerig, J. Lieberman, D. Jones, D. Weinberger: Statistical '''shape''' '''analysis''' of neuroanatomical structures based on medial models, Medical Image '''Analysis''', 7 (3), 2003, pp. 207-220.

@@ Line 15: / Line 15: @@
 [[Image:UNCShape_ShapeCorrespondence.png|thumb|right|300px|]]
-The SPHARM-PDM based correspondence is a global correspondence method that does performs well for many structures. But in our studies it has shown to be inferior to population based correspondence methods, when assessing statistical modeling properties derived from the established correspondence, such as specificity and generalization ability of a statistical model. Current methodology in population based correspondence is based mainly on minimizing distribution properties of surface point locations and are thus not invariant to alignment. We have extended the population based correspondence framework to include curvature based measurements, such as the Koenderink '''Shape''' Index S and Curvedness C in combination with the standard location information. The implementation is based on ITK and uses the SPHARM-PDM correspondence as an initialization. We have favorably compared our combined "Curvature + Location" MDL to the standard MDL, as well as to the SPHARM approach. Especially with more complex structures, such as the femural bone and the striatal structure (composed of caudate, nucleus accumbens and putamen), our method outperforms the other methods. It also illustrates the potential of this approach of objects as complex as the human cortex, the object of our study in the NAMIC year 07/08.
+The SPHARM-PDM based correspondence is a global correspondence method that does performs well for many structures. But in our studies it has shown to be inferior to population based correspondence methods, when assessing statistical modeling properties derived from the established correspondence, such as specificity and generalization ability of a statistical model. Current methodology in population based correspondence is based mainly on minimizing distribution properties of surface point locations and are thus not invariant to alignment. We have extended the population based correspondence framework to include curvature based measurements, such as the Koenderink '''Shape''' Index S and Curvedness C in combination with the standard location information. The implementation is based on ITK and uses the SPHARM-PDM correspondence as an initialization. We have favorably compared our combined "Curvature + Location" MDL to the standard MDL, as well as to the SPHARM approach. Especially with more complex structures, such as the femural bone and the striatal structure (composed of caudate, nucleus accumbens and putamen), our method outperforms the other methods. It also illustrates the potential of this approach of objects as complex as the human cortex, the object of study in the NAMIC year 07/08.
 == Statistics ==