Projects:ShapeAnalysisFrameworkUsingSPHARMPDM - Revision history

Jibberger at 13:44, 21 June 2012

2012-06-21T13:44:38Z

Jibberger at 13:43, 21 June 2012

2012-06-21T13:43:48Z

Bpaniagua: /* UNC-Utah Shape Analysis Framework */

2011-10-25T12:35:57Z

UNC-Utah Shape Analysis Framework

Bpaniagua at 12:35, 25 October 2011

2011-10-25T12:35:00Z

Styner: /* Publications */

2011-04-14T13:31:34Z

Publications

Styner: /* Publications */

2011-04-14T13:30:44Z

Publications

L.bompard: /* Description */

2011-04-01T21:13:53Z

Description

L.bompard: /* Description */

2011-04-01T20:43:07Z

Description

L.bompard: /* Description */

2011-04-01T20:26:29Z

Description

L.bompard: /* Description */

2011-04-01T20:26:17Z

Description

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 [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|thumb|300px|]]
-The UNC shape analysis is based on an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. In summary, the input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes and a minimal smoothing operation. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T^2 two sample metric. An alternative testing framework applies first a Generalized Linear Model and performs testing via a MANCOVA based test statistics. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. The spherical parametrization allow also the calculation of segmentations' medial axis.
+The UNC shape analysis is based on an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. In summary, the input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes and a minimal smoothing operation. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T^2 two sample metric. An alternative testing framework applies first a Generalized Linear Model and performs testing via a MANCOVA based test statistics. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. The spherical parametrization allow also the calculation of the medial axis of the segmentations.
 The implementation has reached a stable framework and has been disseminated to several collaborating labs within NAMIC (BWH, GeorgiaTech, Utah) and many else outside of NAMIC.

@@ Line 5: / Line 5: @@
 [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|thumb|300px|]]
-The UNC shape analysis is based on an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. In summary, the input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes and a minimal smoothing operation. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T^2 two sample metric. An alternative testing framework applies first a Generalized Linear Model and performs testing via a MANCOVA based test statistics. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information.
+The UNC shape analysis is based on an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. In summary, the input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes and a minimal smoothing operation. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T^2 two sample metric. An alternative testing framework applies first a Generalized Linear Model and performs testing via a MANCOVA based test statistics. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. The spherical parametrization allow also the calculation of segmentations' medial axis.
 The implementation has reached a stable framework and has been disseminated to several collaborating labs within NAMIC (BWH, GeorgiaTech, Utah) and many else outside of NAMIC.

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 = UNC-Utah Shape Analysis Framework =
 The UNC-Utah shape analysis project uses a combined methodology of SPHARM-PDM and [[Projects:ParticlesForShapesAndComplexes | entropy-based particle correspondence]] in order to compute reliable correspondences in otherwise challenging biological shapes. SPHARM-PDM solves the correspondence problem by defining a first order ellipsoid aligned, uniform spherical parameterization for each object with correspondence established at equivalently parameterized points. However, SPHARM correspondence has shown to be inadequate for some biological shapes that are not well described by a uniform spherical parameterization. Entropy-based particle systems compute correspondence by representing surfaces as discrete point sets that does not rely in any inherent parameterization. However, they are sensitive to initialization and have little ability to recover from initial errors. The combined framework is implemented as a stand-alone Slicer3 module, which works as an end-to-end shape analysis module.
 = Key Investigators =

@@ Line 22: / Line 22: @@
 Current modifications are focused on improving the Slicer visualizations, as well as enhancing the shape analysis pipeline to follow up SPHARM-PDM correspondence by a [[Projects:ParticlesForShapesAndComplexes |particle based entropy correspondence]]. The resulting surface are analyzed the exact same way as before, but with an improved correspondence.
-[[Image:QC_ShapeAnalysisModule_PhiColorMap.jpeg|thumb|center|900px|shapeAnalysisModule: quality control with phi colormap]]
+[[Image:Spharm-particle.png|thumb|900px| a) SPHARM representation of a neonatal LV, color coded using the spherical parameterization b) Particle set computed using the SPHARM representation triangulated mesh as initialization]]
 = Key Investigators =

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 = Publications =
 ''In Print''
-* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AShapeAnalysisFrameworkUsingSPHARMPDM| NA-MIC Publications Database on Shape Analysis Framework using SPHARM-PDM]
+* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AShapeAnalysisFrameworkUsingSPHARMPDM NA-MIC Publications Database on Shape Analysis Framework using SPHARM-PDM]
 = Links =

← Older revision		Revision as of 21:13, 1 April 2011
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−	[[Image:~~shapeAnalysisModule_theta_mrml~~.~~jpg~~\|thumb\|center\|900px\|shapeAnalysisModule: quality control with ~~theta~~ colormap]]	+	[[Image:QC_ShapeAnalysisModule_PhiColorMap.jpeg\|thumb\|center\|900px\|shapeAnalysisModule: quality control with phi colormap]]

	= Key Investigators =		= Key Investigators =

← Older revision		Revision as of 20:43, 1 April 2011
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−	[[Image:~~shapeAnalysisModule_phi_mrml~~.jpg\|thumb\|center\|900px\|]]	+	[[Image:shapeAnalysisModule_theta_mrml.jpg\|thumb\|center\|900px\|shapeAnalysisModule: quality control with theta colormap]]

	= Key Investigators =		= Key Investigators =

← Older revision		Revision as of 20:26, 1 April 2011
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−	[[Image:shapeAnalysisModule_phi_mrml.jpg\|thumb\|center\|~~600px~~\|]]	+	[[Image:shapeAnalysisModule_phi_mrml.jpg\|thumb\|center\|900px\|]]

	= Key Investigators =		= Key Investigators =