SUPRA: Software Defined Ultrasound Processing for Real-Time Applications - An Open Source 2D and 3D Pipeline from Beamforming to B-Mode
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README.md

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SUPRA: Open Source Software Defined Ultrasound Processing for Real-Time Applications

By the Chair for Computer Aided Medical Procedures

TUM

Main contributors:

  • Rüdiger Göbl
  • Dr. Christoph Hennersperger

Supported by EDEN2020

EDEN2020 Logo

A 2D and 3D Pipeline from Beamforming to B-mode

SUPRA is an open-source pipeline for fully software defined ultrasound processing for real-time applications. Covering everything from beamforming to output of B-Mode images, SUPRA can help reproducibility of results and allows modifications to the image acquisition.

Including all processing stages of a usual ultrasound pipeline, it can be executed in 2D and 3D on consumer GPUs in real- time. Even on hardware as small as the CUDA enabled Jetson TX2 SUPRA can be run for 2D imaging in real-time.

Standard ultrasound pipeline and where the processing takes place. Transmit beamforming is performed on the CPU, transmit and receive are performed in specialized hardware. All other processing steps (receive beamforming, envelope detection, log-compression, scan-conversion) happen in software and on the GPU

License

LGPL v3 see LICENSE

Publication

If you use SUPRA for your research, please cite our work https://doi.org/10.1007/s11548-018-1750-6

Göbl, R., Navab, N. & Hennersperger, C. , "SUPRA: Open Source Software Defined Ultrasound Processing for Real-Time Applications" Int J CARS (2018). https://doi.org/10.1007/s11548-018-1750-6

@Article{Goebl2018supra,
	author="G{\"o}bl, R{\"u}diger and Navab, Nassir and Hennersperger, Christoph",
	title="SUPRA: open-source software-defined ultrasound processing for real-time applications",
	journal="International Journal of Computer Assisted Radiology and Surgery",
	year="2018",
	month="Mar",
	day="28",
	issn="1861-6429",
	doi="10.1007/s11548-018-1750-6",
	url="https://doi.org/10.1007/s11548-018-1750-6"
}

Building

Requirements

  • cmake ≥ 3.4
  • gcc ≥ 4.8 or min. Visual Studio 2015
  • QT ≥ 5.5
  • TBB
  • CUDA ≥ 7.0

Build instructions (Ubuntu 16.04 / 17.10)

Only 17.10: Install GCC 6 (or any other version lower), as 6.3 is latest supported by CUDA 9.0

sudo apt-get install gcc-6 g++-6

Install CMake (≥ 3.4): (installs 3.5 or up on current 16.04, and 3.9 on 17.10)

sudo apt-get install cmake cmake-gui

Install QT dev libraries (≥ 5.5):

sudo apt-get install qt5-default

Install Intel Thread Building Blocks

sudo apt-get install libtbb-dev

Install CUDA (≥ 7.0) as described by NVIDIA https://developer.nvidia.com/cuda-downloads . Keep in mind that the C++ host compiler has to be supported by the CUDA version. (Check http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html and http://docs.nvidia.com/cuda/cuda-installation-guide-microsoft-windows/index.html for details.)

Build OpenIGTLink (OPTIONAL, but recommended)

sudo apt-get install git
mkdir -p $HOME/git && cd $HOME/git #(or your favorite directory for repositories)
git clone https://github.com/openigtlink/OpenIGTLink.git
cd OpenIGTLink
git checkout release-2.1
mkdir -p build && cd build
cmake -D BUILD_TESTING=OFF ..
make -j5
cd $HOME/git

SUPRA

sudo apt-get install git
mkdir -p $HOME/git && cd $HOME/git #(or your favorite directory for repositories)
git clone https://github.com/IFL-CAMP/supra.git
cd supra
mkdir -p build && cd build
cmake-gui ..
  1. Configure

  2. For systems with multiple gcc versions, make sure to select one supported by the installed CUDA version

  3. You might need to specify the CUDA toolkit directory (usually "/usr/local/cuda")

  4. Specify OpenIGTLink build directory for OpenIGTLink_DIR

  5. Configure & Generate, then close cmake and build

  6. Build SUPRA

    make -j5

  7. Start SUPRA: See below

Demo (No US-system required!)

Change to your build directory. If you used the commands above, you can execute

cd $HOME/git/supra/build

Start the SUPRA GUI with a demo config file

src/GraphicInterface/SUPRA_GUI -c data/configDemo.xml -a

Where -c defines the config file to load and -a is autostart.

This shows a complete ultrasound pipeline running on your computer from raw channel data recorded with a Cephasonics system and a 7MHz linear probe. With the dropdown menu "Preview Node", you can select which stage of the pipeline to inspect. For the final state of the image, select "SCAN", which shows the output of the scan-converter - the B-mode.

Used libraries

SUPRA uses tinyxml2 which is awesome and distributed under the zlib-license. For more details see the tinyxml2 README and (http://grinninglizard.com/tinyxml2/index.html and https://github.com/leethomason/tinyxml2)

On windows, ROS-message headers generated with rosserial are used and are included in the source. On Linux, the usual ROS-libraries are used during build. (roscpp, geometry_msgs)

SUPRA additionally uses the Intel Thread Building Blocks (but does not provide them) in their Apache 2.0 licensed form. https://www.threadingbuildingblocks.org/

Finally, it can be built against

  • QT (LGPLv3)
  • IGTL (BSD 3clause)
  • CAMPVis (Apache 2.0) (unfortunately, the respective QT5 version is not yet public)

Acknowledgement

SUPRA logo by Raphael Kretz.

EU flag

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 688279.