2010 Winter Project Week SegmentationMeshEmbeddedContours - Revision history

Pkarasev: /* Key Investigators */

2010-04-07T02:35:03Z

Key Investigators

Pkarasev at 16:08, 8 January 2010

2010-01-08T16:08:59Z

Pkarasev: /* Key Investigators */

2010-01-08T16:06:52Z

Key Investigators

Pkarasev at 16:01, 8 January 2010

2010-01-08T16:01:52Z

Pkarasev: /* Key Investigators */

2010-01-08T15:59:55Z

Key Investigators

Pkarasev at 16:37, 5 December 2009

2009-12-05T16:37:57Z

Pkarasev: /* References */

2009-12-05T15:58:57Z

References

Pkarasev: Created page with 'NOTOC Image:PW-SLC2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

2009-12-05T15:57:07Z

Created page with '__NOTOC__ <gallery> Image:PW-SLC2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

New page

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Key Investigators==
* Georgia Tech: Peter Karasev, Matias Perez, Allen Tannenbaum
* BWH: Ron Kikinis

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing methods for ...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for analyzing is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Software for ...

</div>
</div>

<div style="width: 97%; float: left;">

==References==
... SPIE to appear
</div>

@@ Line 47: / Line 47: @@
 <gallery>
-Image:structure.png|Current Internal Data Structures of Module
+Image:structure.png|Pipeline of vtkPolyDataAlgorithm subclasses encapsulating module internals.
 </gallery>

@@ Line 46: / Line 46: @@
 However the internals are functional, so it was decided that the priority is the *external* interface, which should look like a pipeline of vtkPolyDataAlgorithms, as shown below.
-[[File:structure.png]]
+<gallery>
 The result is that the module code SparseFieldLevelSetContour.cxx used to interface with the module goes from including 8 header files and having access to low-level implementation details to including only one header. The included header contains a namespace with non-member non-friend functions with overloaded entry points to the module.
-The module pipeline now contains three classes that extend vtkPolyDataAlgorithm.
+The module pipeline now contains three classes that extend vtkPolyDataAlgorithm. It now makes use of vtkSmartPointer.
 * vtkInitClosedPath : take in poly data and set of fiducial points, create a closed path including the closest points on the mesh to the given fiducials. Searches for pre-existence of geometry information, pass-through if it already exists.
@@ Line 64: / Line 66: @@
 . Much improved knowledge of linux development, particularly being able to execute the various scripts for Slicer without doing getbuildtest.tcl; saves time.
 </div>

@@ Line 39: / Line 39: @@
 As part of the restructuring effort, a data structure outline of the internals of the module has been made. It makes obvious some aspects that should be refactored.
-[[File:currentform.png]]
+<gallery>
 However the internals are functional, so it was decided that the priority is the *external* interface, which should look like a pipeline of vtkPolyDataAlgorithms, as shown below.

@@ Line 35: / Line 35: @@
 <h3>Progress</h3>
-A version of this software exists in Slicer3, with a standalone version being updated to encapsulate the functionality as a vtkPolyDataFilter. It has been experimentally verified to give useful segmentation results for meshes involving bone fractures (separating smooth non-fracture surface from jagged break zone). Some of the robustness issues (mesh connectivity, neighborhood sizes, differentiable basis functions) that have been seen to make a user experience inconsistent have been formulated as mathematical problems, allowing provable algorithm improvements to move forward. </div>
+A version of this software exists in Slicer3, with a standalone version being updated to encapsulate the functionality as a vtkPolyDataFilter. It has been experimentally verified to give useful segmentation results for meshes involving bone fractures (separating smooth non-fracture surface from jagged break zone). Some of the robustness issues (mesh connectivity, neighborhood sizes, differentiable basis functions) that have been seen to make a user experience inconsistent have been formulated as mathematical problems, allowing provable algorithm improvements to move forward.
 </div>

@@ Line 9: / Line 9: @@
 ==Key Investigators==
-* Georgia Tech: Peter Karasev, Matias Perez, Allen Tannenbaum
+* Georgia Tech: Peter Karasev, Karol Chudy, Allen Tannenbaum
 * BWH: Ron Kikinis

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
-Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
+Image:BrainH.png|Surface Mean Curvature
-Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
+Image:Sulci6_done2.png|Converged Contour Surrounding Region
 </gallery>
 ==Key Investigators==
@@ Line 15: / Line 16: @@
 <h3>Objective</h3>
-We are developing methods for ...
+We are developing methods for segmentation of surfaces defined by polygonal meshes. In image or volume-slice segmentation, 'information' comes from image intensity, while in mesh surface segmentation the information is purely geometric. The goal of this project is to develop algorithms allowing a user to quickly and robustly segment one or several regions on a surface. Specifically, it is required to reconcile some concepts in classical differential geometry and embedded curves with the numerical and discrete-space constraints of polygon meshes.
@@ Line 28: / Line 26: @@
 <h3>Approach, Plan</h3>
-Our approach for analyzing is <foo>.
+Our approach for analyzing surface-embedded segmentation is separated into two parts. First, the notion of surface geometry for a polygonal mesh must be suitably defined. To this end, we study numerically stable and robust methods of estimating the geometry of the surface (mean curvature, tangent plane bases, second fundamental form, etc) and that of the segmenting curve. Second, we explore definitions of functionals whose extrema lead to useful geometric flows on the surface. The techniques for these two tasks must always consider the difficulty imposed by data purely in the form of a polygon mesh. This project makes extensive use of the VTK library to simplify data storage, communication, and visualization.
-Our plan for the project week is to first try out <bar>,...
+Our plan for the project week is to first come up with the best encapsulation framework for data storage and persistence, making the existing Slicer3 implementation feature-complete. Secondly, we seek to explore reformulation of existing image volume segmentation and mesh generation such that the numerical stability and accuracy of subsequent surface segmentation is taken into consideration.
 </div>
@@ Line 37: / Line 35: @@
 <h3>Progress</h3>
-Software for ...
+A version of this software exists in Slicer3, with a standalone version being updated to encapsulate the functionality as a vtkPolyDataFilter. It has been experimentally verified to give useful segmentation results for meshes involving bone fractures (separating smooth non-fracture surface from jagged break zone). Some of the robustness issues (mesh connectivity, neighborhood sizes, differentiable basis functions) that have been seen to make a user experience inconsistent have been formulated as mathematical problems, allowing provable algorithm improvements to move forward. </div>
 </div>

@@ Line 46: / Line 46: @@
 ==References==
-... SPIE to appear
+P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
 </div>

2010 Winter Project Week SegmentationMeshEmbeddedContours - Revision history

Pkarasev: /* Key Investigators */

Pkarasev at 16:08, 8 January 2010

Pkarasev: /* Key Investigators */

Pkarasev at 16:01, 8 January 2010

Pkarasev: /* Key Investigators */

Pkarasev at 16:37, 5 December 2009

Pkarasev: /* References */

Pkarasev: Created page with '__NOTOC__ Image:PW-SLC2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

Pkarasev: Created page with 'NOTOC Image:PW-SLC2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'