Revision as of 16:40, 19 October 2010

Stephen

Implementation on the ComputeTortuosity module (only Distance Metric)
- Started debugging

Future
- More debugging! ---> hopefully testing soon
- #tube command
- Implementation of the other 2 methods : ICM SOAM

Fixed "duh" problem from Thursday - extracting tangential and normal components before computing regularization
Regularization smoothing in normal direction completed
Added intensity distance function (mean squares)

Got XCAT running on my machine (thanks Andinet!)
Learned XCAT parameters
Wrote isbiValidation.py:
- --basic (XCAT mode 0 - phantom mode): with respiratory period 5s and cardiac period 1s, generates two images at 0s and 2.5 s, saves as .mhd
- --gold (XCAT mode 2 - spherical lesion generation mode): creates gold standard motion field, and saves as .txt (index, vector in 6 columns). Then run itkImageToImageDiffusiveDeformableRegistrationGenerateGoldStandardTest to create itk::Image<VectorType, Dimension> .mhd for visualization
  - XCAT phantom gives gold standard vectors for surface borders (XCAT mode 4), but no internal vectors! So...
  - for index in range - generate spherical lesion at index, use nurbs_save = 1 to save lesion.nrb, then calculate centroid of lesion control points

- --segmentation (XCAT mode 0 - phantom mode): with nurbs_save = 1 to save surfaces (.nrb text file). Then create new .txt file for the surface you want. Then run itkImageToImageDiffusiveDeformableRegistrationGenerateNormalsTest to create itk::Image<PixelType, Dimension> of control points
  - Unfortunately: (1) control points need interpolation, can't find NURBS support in VTK; (2) XCAT has MANY types of surfaces for one organ - ex all intracardiac surfaces, etc, and it would be a lot of work to sort through them; (3) Perfect segmentation not great for registration method evaluation - removes segmentation error component of total error.

Underlying XCAT deformation fields too perfect? They are likely interpolating the border vectors.

@@ Line 42: / Line 42: @@
 *** XCAT phantom gives gold standard vectors for surface borders (XCAT mode 4), but no internal vectors!  So...
 *** for index in range - generate spherical lesion at index, use nurbs_save = 1 to save lesion.nrb, then calculate centroid of lesion control points
+[[File:goldStandardMotionFieldScreenshot.png]]
 ** --segmentation (XCAT mode 0 - phantom mode): with nurbs_save = 1 to save surfaces (.nrb text file).  Then create new .txt file for the surface you want.  Then run itkImageToImageDiffusiveDeformableRegistrationGenerateNormalsTest to create itk::Image<PixelType, Dimension> of control points
 *** Unfortunately: (1) control points need interpolation, can't find NURBS support in VTK; (2) XCAT has MANY types of surfaces for one organ - ex all intracardiac surfaces, etc, and it would be a lot of work to sort through them; (3) Perfect segmentation not great for registration method evaluation - removes segmentation error component of total error.