AHM2012-3D-US-Slicer-Breakout

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Objective

The objective of this break out session is discuss 1) the current Slicer activities related to ultrasound guided therapies, 2) identify shared interest effort overlap, and common unmet needs, 3) produce common statement from participants about the action plans. Everyone is welcome to attend.

Time/Date/Place

  • In 2012 NA-MIC all hands meeting
  • 8:10-12:00, Wednesday, January 11, 2012
  • Amethyst room, Marriott, Salt Lake City, UT

Coordinator

  • Nobuhiko Hata, PhD, Brigham and Women's Hospital
  • Andras Lasso, PhD, Queens University

Agenda

  • 8:10-8:20, Welcome, Goal of the meeting, Meeting logistics, Note taking in wiki
  • 8:20-8:35, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso (slides)
    • Keywords: Plus framework, applications, spatial & temporal calibration, volume reconstruction, ECG
  • Project introduction 2, Tamas Ungi, Tracked real-time 2D ultrasound in Slicer (LiveUltrasound) (slides)
    • Keywords: OpenIGTLink, needle guidance
  • Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging. The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. We want to integrate the BK RF streaming module with the PLUS/Slicer development.
  • short break
  • Project introduction 3, Elvis Chen, GPU volume rendering. We have developed (clean room implementation) a stand-along, CUDA-based, VTK class for volume rendering. It is meant to be a drop-in replacement for vtkVolumeMapper. In addition, we implemented multi-dimentional transfer function, allowing much concise pixel-classification and visualization. Video demo will be given, source code will be made available.
    • Keywords: CUDA, volume rendering, transfer function
  • Project introduction 4, Laurent Chauvin, 4D US rendering
    • Keywords: 4D volume rendering, recording/replay
  • Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
    • Keywords: OpenIGTLink, 4D Image Module
  • Project introduction 7, Nobuhiko Hata, review of U.S. US efforts
    • Keyword: JHU efforts, BWH efforts, more...


  • 11:00-11:30, Summary of current US projects, Breakdown of core technologies, Identifying unmet needs,
  • 11:30-12:00, Group statement, Action Plan, Plan for the next events

Meeting minutes

  1. Andras presentation
  2. PLUS library
  3. Based on Synchrograb
  4. Acquire, process, transfer synchronized ultrasound images and position data
  5. Specialized Open IGT Link QueensOpenIGTLibs
  6. Separate effort from OPEN IGT Link
  7. [NH question] any effort toward integration
  8. 4D Ultrasound module in NAMIC sandbox repository (*)
  9. Features: calibration (*), B-mode imaging capturing (video?) RF?, support for multiple hardware devices
  10. Sample data can be incorporated w/o hardware
  11. Supported hardware (not defined well, but sounds very attractive to most of the investigators)
  12. Standalone solution: Device SDK, and drivers
  13. 3D Slicer module
  14. Temporal calibration
  15. Change detection methods
  16. Correlation-based (**)
  17. Correct 150 msec
  18. File format sequence metafile….. **** we need I/O for this in Slicer, we need module in Slice to handle this kind of data
  19. Question… effort to visualize 4D data in Slicer, frames grabbed how does this relates to 4D Volume, or shall we handle this as single frame?
  20. 2D+t as primitive needed in Slicer?
  21. Logging ---- within library


  1. Tamash
  1. PLUS image acquisition and data transfer to Slicer
  2. Open IGT Link send cords of needle and image
  3. 2D image primitive with vtkImage updated
  4. images are thrown away
  1. What is needed
  2. Tracker-model registration module, OR IGT transformation module
  3. Time
  4. Recording / replay functions
  5. Mehdi Moradi
  6. Prostate cancer
  7. Elastography. Not so much in Slicer. Good platform for translational research
  8. Technical issue
  1. Elvin Cheng
  2. VTK Volume Rendering using CUDA
  3. CUDA capable video , CUDA capable driver, SDK,
  4. Qt
  5. Implementation to Slicer 4 in plan
  6. Widget support for multi-dimensional transfer function = CTK
  7. Transfer-function tuning
  1. Junchi Tokuda presented
  2. 4D module, which bundles multiple volumetric data (stored in MRML) and create a 4D volume
  3. DWI users of 4D image dataset per se.
  4. Population study uses 3D + N
  1. We agreed that the two approaches should be tried
  2. DWI based approach where one MRML node contains all images
  3. Junichi’s node where multiple separate volume is bundled


Plus

  • IGSTK similar
  • windows-only
  • DirectShow video source

OpenIGTLink

  • single-slice display: similar in LiveUltrasound and OpenIGTLinkIF module => in Slicer4 OpenIGTLinkIF should be enough

Ultrasound for tissue characterization

  • 2D+t ultrasound (B or RF) for tissue characterization, elastography
  • Problems
    • No access to Nucletron's brachy stepper
    • No access to many ultrasound imaging devices


4D data - overlapping efforts!

  • 4D node:
    • DWI-like
    • DCE-MRI
  • bundle node with pointers
    • 4D ultrasound
    • 4D images
    • bundles of bundles, arbitrary paremeters (not just t), arbitrary nodes, arbitrary number of bundles could be possible
  • time (parameter) points should be stored: there could be a subclass with additional
  • custom data IO would be useful for sequence metafiles, NRRD files or other xD+t file formats

Volume rendering

  • Elvis' GPU renderer=> discuss with Julien Finet
  • streaming data to GPU is challenging
  • CUDA-only is a limitation (no MacOS, NVidia-only), OpenCL would be betterbetter
    • could we bypass CPU?
    • image source is coming from Ethernet, that could be a bottleneck
    • if volume has to be imported into Slicer then the data should be in RAM, not enough to directly send to GPU

Use cases

  • TEE-guided surgery
  • 2D+t live ultrasound
  • 2D+t ultrasound (B or RF) for tissue characterization, elastography
  • 4D US/MRI registration
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