2010 Summer Project Week SegmentationMeshEmbeddedContours - Revision history

Pkarasev: /* Key Investigators */

2010-06-25T14:30:52Z

Key Investigators

Pkarasev: /* Key Investigators */

2010-06-25T14:23:33Z

Key Investigators

Pkarasev: /* Key Investigators */

2010-06-25T14:05:32Z

Key Investigators

Pkarasev at 13:58, 25 June 2010

2010-06-25T13:58:02Z

Pkarasev: /* Key Investigators */

2010-06-25T13:37:35Z

Key Investigators

Pkarasev: /* Key Investigators */

2010-06-25T13:17:21Z

Key Investigators

Pkarasev: /* Key Investigators */

2010-06-25T12:58:58Z

Key Investigators

Pkarasev: /* Key Investigators */

2010-06-05T18:56:04Z

Key Investigators

Pkarasev at 18:54, 5 June 2010

2010-06-05T18:54:33Z

Pkarasev: /* Key Investigators */

2010-06-05T18:50:32Z

Key Investigators

@@ Line 46: / Line 46: @@
 </div>
-<div style="width: 40%; float: right;">
 <h3>Progress</h3>
@@ Line 103: / Line 104: @@
-</div>
+Some implementation specifics
 Development is much easier now for two reasons:
@@ Line 164: / Line 160: @@
+}
 </pre>
 ==References==
 P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.
 </div>

@@ Line 14: / Line 14: @@
 * BWH: Ron Kikinis
-<h3>Update</h3>
+</div>
 . Setup Slicer4 "superbuild", verified module consistency therein
@@ Line 72: / Line 103: @@
 </div>
-* vtkLevelSetMeshEvolver : take in poly data with a scalar array defining the current region boundaries. Update the boundaries with curve evolution and return poly data with updated scalar array.
+<h3> Some implementation specifics </h3>
 Development is much easier now for two reasons:
@@ Line 177: / Line 164: @@
+}
 </pre>
 ==References==
 P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. SPIE Medical Imaging 2010.
 </div>

@@ Line 23: / Line 23: @@
      i. large neighborhood curvature computation via paraboloid fit
      ii. unstructured graph sparse field level sets )
-. From discussion with Ron Kikinis and Karl Fritter, going forward must branch the functionality:
+. From discussion with Ron Kikinis and Karl Fritscher, going forward must branch the functionality:
      i. don't compute 'global geometry' in Slicer, must look up neighbors as needed as user is only segmenting a small piece of large mesh
      ii. allow more geometric information to be returned and stored for statistical analysis and registration of surfaces

@@ Line 6: / Line 6: @@
 Image:Sulci3_init_3.png|Initial Points From User
 Image:bone-end3.png|Segmenting Tibia Fracture via Surface Geometry
 </gallery>

@@ Line 21: / Line 21: @@
      i. large neighborhood curvature computation via paraboloid fit
      ii. unstructured graph sparse field level sets )
-.
+. From discussion with Ron Kikinis and Karl Fritter, going forward must branch the functionality:
 . Curvature overlay in Slicer:

@@ Line 11: / Line 11: @@
 * Georgia Tech: Peter Karasev, Karol Chudy, Allen Tannenbaum
 * BWH: Ron Kikinis
 <h3>Update</h3>
 Implemented a helpful re-factor, convert a beefy struct with bunch of global functions to a class with member functions plus non-member non-friend helper functions in anonymous namespace
 <pre>
@@ Line 46: / Line 61: @@
 </pre>
 <div style="margin: 20px;">

@@ Line 31: / Line 31: @@
 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.
-At the moment, the modules documentation and code can be found at the [http://www.slicer.org/slicerWiki/index.php/Modules:MeshContourSegmentation-Documentation-3.6]. Using a series of data structures and algorithms outlined below, we calculate the best fit curve that encapsulates all of the users self-chosen fiducial points. Through a series of iterations in our closed-path algorithm, we continuously select vertices that are equidistant from existing path points and add them to our path data structure. By running this algorithm until our path, and therefore segmentation selection, consists of a closed group of points, we can highlight a region with as little as 3 points after enough iterations.
+At the moment, the modules documentation and code can be found at the it's relative Slicer Documentation page.[http://www.slicer.org/slicerWiki/index.php/Modules:MeshContourSegmentation-Documentation-3.6]. Using a series of data structures and algorithms outlined below, we calculate the best fit curve that encapsulates all of the users self-chosen fiducial points. Through a series of iterations in our closed-path algorithm, we continuously select vertices that are equidistant from existing path points and add them to our path data structure. By running this algorithm until our path, and therefore segmentation selection, consists of a closed group of points, we can highlight a region with as little as 3 points after enough iterations.  Once the path is closed we can select all of the points inside of it and add them to our selection data structure.
 To obtain consistent results we smooth out our 'organic blob' of points through a series of iterations, trying to minimize the total curvature of the closed path. This makes it so that our selection doesn't stop in the middle of say, a ridge or bump, but will encapsulate what the user is most likely trying to segment.
@@ Line 40: / Line 38: @@
-Previous Notes:
+<h3>Previous Notes:</h3>
 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.

@@ Line 8: / Line 8: @@
 </gallery>
-'''Bold text'''==Key Investigators==
+== Key Investigators ==
 * Georgia Tech: Peter Karasev, Karol Chudy, Allen Tannenbaum
 * BWH: Ron Kikinis
 <div style="margin: 20px;">
-<div style="width: 27%; float: left; padding-right: 3%;">
+<div style="width: 37%; float: left; padding-right: 3%;">
 <h3>Objective</h3>
@@ Line 91: / Line 91: @@
 <pre>
 // Input: mesh and indices of vertices for initialization
-vtkPolyData* MeshContourEvolver::entry_main( vtkPolyData* inputMesh, const vector<int>& initPointVertexIndices )
+vtkPolyData* MeshContourEvolver::entry_main( vtkPolyData* inputMesh,
+{
 	// instantiate output mesh