TubeTK/Events/2010.07.26: Difference between revisions

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= Andinet =
* Primary goal: Data from Duke for BWH
* Accomplishments
** Attend NAMIC AHM
** Determine what is necessary to record data sent to OpenIGTLink from VectorVision system
*** Define data workflow and software architecture
*** Begin implementation
*** Product: powerpoint presentation: 5 slides
* Near term (August 1)
** Install VV at Duke
** Determine if we can get US data from Duke machine
** Write IJ article
*** Cite grant proposal in article
* Medium term (1.5 months, August 15)
** Investigate simulation of ultrasound from MR/CT (Talk to Stephen First :) )
** Code review of vessel segmentation method from Stephen
= Patrick =
= Patrick =
* Primary goal: Bump and dent identification on IC images
* Primary goal: Bump and dent identification on IC images
Line 64: Line 47:
** Complete port and test of existing adjacency code
** Complete port and test of existing adjacency code
*** Prepare IJ article
*** Prepare IJ article
= Andinet =
* Primary goal: Data from Duke for BWH
* Accomplishments
** Data from Duke
*** Contacted several folks to gather information ( we had
questions regarding the machine at Duke) and check status.
**** BrainLab: Contacted Pratik. He is working on getting us VV license
**** Duke: Contacted Tanya and learned that SD-5000  ultrasound machine is not integrated with the BrainLab system. The machine is used to acquire ultrasound data independently.
**** Aloka: Contacted John Walsh at Aloka and learned that SD-5000 is very old model and doesn't come with research interface
*** Based upon the conversation I had with you, may be we should probably look into saving data off the BrainLab system itself not bother with the SD-5000.
** Write IJ article
*** Hua and I have made progress writing the IJ article. Hua helped me a lot generating results using synthetic data. We have now a solid outline and some write up in most of the sections. We will add more texts, figures and results and clean it up more. I will also put together self-contained source code tree containing the classes that we will submit with this paper Please see attached the latest version.
*** You can also access the tex, bib, etc files in my Work directory: Work/Andinet/TensorIJ
* Near term (August 2)
** Move article to TubeTK/Documentation/2010.TensorIJ
*** Cite grant proposal in article
** Install VV at Duke
* Medium term (August 9)


= Hua =
= Hua =
* Primary goal: ultrasound image processing
* Primary goal: ultrasound image processing
* Accomplished
* Accomplished
** Verify Andinet's code: add tests and help with IJ publication
** Correct a bug in itkAnisotropicHybridDiffusionImageFilter, and prepared figures for Andinet's Insight Journal paper.
*** Creating tests (sin pattern with known derivatives)
** Improve code coverage for uncovered filters under Application/CLI/** Increase coverage of TubeTK
* Near term (August 1)
* Near term (August 2)
** Increase coverage of TubeTK
** Update registration code
** Update registration code
** Begin investigation of registration metrics that depend on ultrasound probe orientation
** Begin investigation of registration metrics that depend on ultrasound probe orientation
*** Get data from InnerOptic
*** Get data from InnerOptic
**** Design phantom or use something from InnerOptic
**** Discuss with InnerOptic
**** CIRS Phantom
**** http://www.insight-journal.org/midas/item/view/2206
**** http://www.insight-journal.org/midas/item/view/2206
**** http://www.insight-journal.org/midas/item/view/117
**** http://www.insight-journal.org/midas/item/view/117
* Medium term (1.5 months
* Medium term (August 16)
** Investigate use of speckle in ultrasound registration
** Investigate use of speckle in ultrasound registration
** Model-based deformation field interpolation
** Model-based deformation field interpolation
** 2D-3D registration (data)
** Simulating ultrasound from MR/CT

Revision as of 16:30, 26 July 2010

Patrick

  • Primary goal: Bump and dent identification on IC images
  • Accomplishments
    • Traveled to SSRL to view the acquisition and meet with Greg and Mike.
    • Modified the GenerateFeatures application to handle the input of arbitrary feature images
    • Using the previous features and Casey's new patch-based features, was able to achieve 95% pixel level accuracy in Weka and 23/25 defects found with 0 false positives in image space (after morphology).
    • Explore new features
      • evaluate a variety of standard deviations for intensity and ridge computations
  • Near Term (Aug 2)
    • Receiving code to simulate the tomography directly on GDS Layers
    • Compute dot-product between line (hessian) tangent and normal directions in ES and GDS images
    • Subselect features
    • Product: ~ 5 slides / report to USC illustrating path chosen, strengths, and weaknesses.
      • Real-world tests / workflow
      • Does a trained classifier work on other layers?
      • Does a trained classifier work on other acquisitions?
        • i.e., do we need to insert modifications for training on every slice / acquisition / ?
        • Normalizing for inter-acquisition (or inter-slice) variations?
    • Work with new collaborator at Kitware.
  • Medium term (August 15)
    • Delivery and education
    • Can we get better in simulation?
    • Connectivity analysis

Casey

  • Primary goal: Compare populations of vascular networks
  • Near term (0.5, Aug 1)
    • Collaborate with Patrick
      • Feature extraction
        • Patch-based features (max, median, quantiles)
        • Scales / neighborhood
      • Feature research
        • Width estimate from Stephen (concern, time)
        • Location of local max in ridgeness
        • Subsample centerlines
        • Optimal match filter
      • Classifiers
        • Comparison
        • Implementation for transfer to USC
        • Hierarchy (Good/bad. If bad, then add/sub.)
    • Data for Retinas
  • Medium term (1 months, Aug 15)
    • Review previous processing pipeline with Stephen
    • Research on methods for comparing spatial graphs / adjacency matrices
    • Begin Port and test existing adjacency code
    • Process retinal data
    • Complete port and test of existing adjacency code
      • Prepare IJ article

Andinet

  • Primary goal: Data from Duke for BWH
  • Accomplishments
    • Data from Duke
      • Contacted several folks to gather information ( we had

questions regarding the machine at Duke) and check status.

        • BrainLab: Contacted Pratik. He is working on getting us VV license
        • Duke: Contacted Tanya and learned that SD-5000 ultrasound machine is not integrated with the BrainLab system. The machine is used to acquire ultrasound data independently.
        • Aloka: Contacted John Walsh at Aloka and learned that SD-5000 is very old model and doesn't come with research interface
      • Based upon the conversation I had with you, may be we should probably look into saving data off the BrainLab system itself not bother with the SD-5000.
    • Write IJ article
      • Hua and I have made progress writing the IJ article. Hua helped me a lot generating results using synthetic data. We have now a solid outline and some write up in most of the sections. We will add more texts, figures and results and clean it up more. I will also put together self-contained source code tree containing the classes that we will submit with this paper Please see attached the latest version.
      • You can also access the tex, bib, etc files in my Work directory: Work/Andinet/TensorIJ
  • Near term (August 2)
    • Move article to TubeTK/Documentation/2010.TensorIJ
      • Cite grant proposal in article
    • Install VV at Duke
  • Medium term (August 9)

Hua

  • Primary goal: ultrasound image processing
  • Accomplished
    • Correct a bug in itkAnisotropicHybridDiffusionImageFilter, and prepared figures for Andinet's Insight Journal paper.
    • Improve code coverage for uncovered filters under Application/CLI/** Increase coverage of TubeTK
  • Near term (August 2)
  • Medium term (August 16)
    • Investigate use of speckle in ultrasound registration
    • Model-based deformation field interpolation