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An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images. Jonathan Boisvert , David Gobbi, Siddharth Vikal, Robert Rohling, Gabor Fichtinger and Purang Abolmaesumi Medical Image Analysis (MedIA) Laboratory http://www.media.queensu.ca

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An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images

Jonathan Boisvert, David Gobbi, Siddharth Vikal, Robert Rohling, Gabor Fichtinger and Purang Abolmaesumi

Medical Image Analysis (MedIA) Laboratory

http://www.media.queensu.ca

Queen’s University

Kingston, Ontario, Canada

http://www.media.queensu.ca


Introduction
Introduction Processing and Transfer of Interventional Ultrasound Images

  • Ultrasound is a very common interventional image modality

    • Open-interface machines makes it even more attractive to IGT developers

  • Often used with motion tracking devices.

  • Problem:

    • Acquisition, synchronization and transfer to existing IGT systems is more difficult than it should be.

http://www.media.queensu.ca


Prior work Processing and Transfer of Interventional Ultrasound Images

  • Integrated navigation software such as:

    • CustusX1, IGSonic2, SonoNav3 or Stradx4.

  • Software frameworks such as:

    • IGSTK5

  • Slicer specific software development

    • A module for Slicer 2 initially developed by Boctor et al.6

http://www.media.queensu.ca


Open-source software platform: Slicer Processing and Transfer of Interventional Ultrasound Images

Sophisticated registration, data-fusion and visualization capabilities

Modular architecture

Multi-platform

Support for the new OpenIGTLink protocol

http://www.media.queensu.ca


Architecture : SynchroGrab Processing and Transfer of Interventional Ultrasound Images

  • Provide real-time ultrasound processing capabilities.

  • Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

http://www.media.queensu.ca


Architecture : SynchroGrab Processing and Transfer of Interventional Ultrasound Images

  • Provide real-time ultrasound processing capabilities.

  • Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

http://www.media.queensu.ca


Architecture : SynchroGrab Processing and Transfer of Interventional Ultrasound Images

  • Provide real-time ultrasound processing capabilities.

  • Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

http://www.media.queensu.ca


Architecture : SynchroGrab Processing and Transfer of Interventional Ultrasound Images

  • Provide real-time ultrasound processing capabilities.

  • Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

http://www.media.queensu.ca


Architecture : SynchroGrab Processing and Transfer of Interventional Ultrasound Images

  • Provide real-time ultrasound processing capabilities.

  • Delegate visualization, registration and navigation to an OpenIGTLink compatible software (Slicer).

http://www.media.queensu.ca


Ultrasound image acquisition Processing and Transfer of Interventional Ultrasound Images

  • SonixRP

    • Open interface

    • Access to pre-scan converted images, post-scan converted images, imaging parameters, RF raw-data, etc.

  • New vtk class “vtkSonixVideoSource”

    • Easy integration

    • Highly reusable

http://www.media.queensu.ca


Using vtkSonixVideoSource Processing and Transfer of Interventional Ultrasound Images

vtkSonixVideoSource *sonixGrabber = vtkSonixVideoSource::New();

sonixGrabber->SetSonixIP("127.0.0.1");

sonixGrabber->SetImagingMode(BMode);

sonixGrabber-> SetAcquisitionDataType(udtBPost);

sonixGrabber->Record();

sonixGrabber->Stop();

sonixGrabber->Rewind();

// Process the first image here

sonixGrabber->Seek(1)

// Process the second image here

sonixGrabber->Delete();

  • Inherit from vtkVideoSource

  • Support many data types:

    • BPreScan, BPost 8 bit, BPost 32 bit, RF 16 bit, MPost 8 bit, Color+ B 32 bits

http://www.media.queensu.ca


3D Tracking Processing and Transfer of Interventional Ultrasound Images

  • Object oriented

  • Extensible

  • Multi-threaded

  • Circular buffers for transformations synchronization

http://www.media.queensu.ca


Synchronization Processing and Transfer of Interventional Ultrasound Images

  • Tracking and ultrasound imaging

    • not performed at the same frequency.

    • Need to interpolate the poses (using spherical linear interpolation)

http://www.media.queensu.ca


Synchronization Processing and Transfer of Interventional Ultrasound Images

  • Data preprocessing

    • Hardware latency, pose computation, ultrasound image processing, and copy to user-space memory.

  • OS related

    • Context switching, memory swapping, etc.

  • Compensate for the mean lag

http://www.media.queensu.ca


Synchronization Processing and Transfer of Interventional Ultrasound Images

  • vtkTaggedImageFilter

    • Compute the transformation associated with an image.

    • Two inputs: a vtkTrackerTool and a vtkImageAlgorithm object

vtkTaggedImageFilter *tagger = vtkTaggedImageFilter::New();

tagger->SetInput(sonixGrabber->GetOutput());

tagger->SetTrackerTool(trackerTool);

tagger->SetTemporalLag(xxx);

tagger->Update();

currentTransforms = tagger->GetTransform();

currentImage = tagger->GetOutput();

http://www.media.queensu.ca


3D Reconstruction Processing and Transfer of Interventional Ultrasound Images

  • Synchronized images and transformation

    • Combined to produce 3D volumes

    • Pixel-based reconstruction

      • Pixel nearest neighbors (PNN)

      • Pixel trilinear interpolation (PTL)

http://www.media.queensu.ca


Reconstructing volumes Processing and Transfer of Interventional Ultrasound Images

Just start the application using the command line

SynchroGrab --calibration-file 071508_162653.Calibration.results --reconstruct-volume --nb-frames 150 --fps 5 --use-tracker-transforms

http://www.media.queensu.ca


Communication with Slicer Processing and Transfer of Interventional Ultrasound Images

  • Real-time acquisition using SynchroGrab.

  • Visualization with Slicer 3.

SynchroGrab --calibration-file 071508_162653.Calibration.results --oigtl-transfert-images --nb-frames 150 --fps 5

http://www.media.queensu.ca


Communication with Slicer Processing and Transfer of Interventional Ultrasound Images

http://www.media.queensu.ca


Conclusion & Future work Processing and Transfer of Interventional Ultrasound Images

  • SynchroGrab

    • Acquisition and synchronization of tracking and ultrasound data

    • Can be used as a stand-alone command-line application.

    • Can be used in conjunction to an OpenIGTLink compliant software.

  • Development of temporal calibration protocols

  • Future support for 3D probes

http://www.media.queensu.ca


References Processing and Transfer of Interventional Ultrasound Images

  • T. Lango, G. A. Tangen, R. Marvik, B. Ystgaard, Y. Yavuz, J. H. Kaspersen, O. V. Solberg, and T. A. N. Hernes. Navigation in laparoscopy–prototype research platform for improved image-guided surgery. Minim Invasive Ther Allied Technol, 17(1):17–33, 2008.

  • BrainLAB (AG, Heimstetten, Germany). IGSonic. http://www.brainlab.com

  • Medtronic(Louisville, CO, U.S.). SonoNav. http://www.medtronicnavigation.com

  • Graham Treece, Richard Prager and Andrew Gee. Stradx/Stradwin. http://mi.eng.cam.ac.uk/~rwp/stradwin/

  • Andinet Enquobahrie, Patrick Cheng, Kevin Gary, Luis Ibanez, David Gobbi, Frank Lindseth, Ziv Yaniv, Stephen Aylward, Julien Jomier, and Kevin Cleary. The image-guided surgery toolkit IGSTK: an open source C++ software toolkit. J Digit Imaging, 20 Suppl 1:21–33, 2007.

  • E. M. Boctor, A. Viswanathan, S. Pieper, M. A. Choti, R. H. Taylor, R. Kikinis, and G. Fichtinger. CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API. Proceedings of the SPIE, volume 5367, pages 247–256, May 2004

http://www.media.queensu.ca


Acknowledgments Processing and Transfer of Interventional Ultrasound Images

  • Natural Sciences and Engineering Research Council (NSERC),

  • Canadian Institutes of Health Research (CIHR),

  • National Alliance in Medical Image Computing (NIH5U54EB005149-03),

  • Fonds québécois de recherche sur la nature et les technologies.

http://www.media.queensu.ca


Questions Processing and Transfer of Interventional Ultrasound Images

http://www.media.queensu.ca


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