An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultra...
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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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Introduction 5650663

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

  • 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


Introduction 5650663

Prior work

  • 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


Introduction 5650663

Open-source software platform: Slicer

Sophisticated registration, data-fusion and visualization capabilities

Modular architecture

Multi-platform

Support for the new OpenIGTLink protocol

http://www.media.queensu.ca


Introduction 5650663

Architecture : SynchroGrab

  • Provide real-time ultrasound processing capabilities.

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

http://www.media.queensu.ca


Introduction 5650663

Architecture : SynchroGrab

  • Provide real-time ultrasound processing capabilities.

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

http://www.media.queensu.ca


Introduction 5650663

Architecture : SynchroGrab

  • Provide real-time ultrasound processing capabilities.

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

http://www.media.queensu.ca


Introduction 5650663

Architecture : SynchroGrab

  • Provide real-time ultrasound processing capabilities.

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

http://www.media.queensu.ca


Introduction 5650663

Architecture : SynchroGrab

  • Provide real-time ultrasound processing capabilities.

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

http://www.media.queensu.ca


Introduction 5650663

Ultrasound image acquisition

  • 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


Introduction 5650663

Using vtkSonixVideoSource

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


Introduction 5650663

3D Tracking

  • Object oriented

  • Extensible

  • Multi-threaded

  • Circular buffers for transformations synchronization

http://www.media.queensu.ca


Introduction 5650663

Synchronization

  • Tracking and ultrasound imaging

    • not performed at the same frequency.

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

http://www.media.queensu.ca


Introduction 5650663

Synchronization

  • 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


Introduction 5650663

Synchronization

  • 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


Introduction 5650663

3D Reconstruction

  • 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


Introduction 5650663

Reconstructing volumes

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


Introduction 5650663

Communication with Slicer

  • 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


Introduction 5650663

Communication with Slicer

http://www.media.queensu.ca


Introduction 5650663

Conclusion & Future work

  • 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


Introduction 5650663

References

  • 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


Introduction 5650663

Acknowledgments

  • 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


Introduction 5650663

Questions

http://www.media.queensu.ca


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