AVIONIC

Accelerated Variational Dynamic MRI Reconstruction

Contributors

• Andreas Schwarzl (Graz University of Technology)
• Martin Holler (University of Graz)
• Matthias Schloegl (Graz University of Technology)
• Kristian Bredies (University of Graz)

License

This software is published under GNU GPLv3. In particular, all source code is provided "as is" without warranty of any kind, either expressed or implied. For details, see the attached LICENSE.

General Information

AVIONIC (Accelerated Variational Dynamic MRI Reconstruction) is an open source software for GPU accelerated reconstruction of hightly undersampled dynamic Magnetic Resonance data, such as functional cardiac imaging oder dynamic contrast enhanced (DCE) MRI applications. It also includes a variational approach for the estimation of receiver-coil sensitivity profiles from the undersampled data. The current version is able to handle Cartesian and Non-Cartesian data if the trajectory information is provided.

If you use this software please cite:

• Matthias Schloegl, Martin Holler, Kristian Bredies, Karl Kunisch, and Rudolf Stollberger. ICTGV Regularization for Highly Accelerated Dynamic MRI. Proc. Intl. Soc. Mag. Reson. Med. 23, Toronto, Canada;

• Matthias Schloegl, Martin Holler, Kristian Bredies, and Rudolf Stollberger. A Variational Approach for Coil-Sensitivity Estimation for Undersampled Phase-Sensitive Dynamic MRI Reconstruction Proc. Intl. Soc. Mag. Reson. Med. 23, Toronto, Canada;

This work is funded and supported by the Austrian Science Fund (FWF) in the context of project 'SFB F3209-19' (Mathematical Optimization and Applications in Biomedical Sciences) MOBIS

For questions and comments on the project please contact Matthias Schloegl

Dependencies

• CUDA 4.0
• CMAKE 2.8
• GCC
• AGILE
• gpuNUFFT
• ISMRMRD
• DCMTK
• Doxygen (for code docs)

Setup

0 Preparations

• Make sure that the CUDA environment is set up correctly
• Ensure that the DCMDICTPATH environment variable is set correctly, namely with
  export DCMDICTPATH=$DCMDICTPATH:/usr/local/share/dcmtk/dicom.dic:/usr/local/share/dcmtk/private.dic

1 Install AGILE lib

git clone https://github.com/IMTtugraz/AGILE.git
cd AGILE
mkdir build
cd build
cmake ..
make -j 
sudo make install

2 Install gpuNUFFT

git clone https://github.com/andyschwarzl/gpuNUFFT.git
cd gpuNUFFT/CUDA
mkdir build
cd build
cmake ..
make

3 Install ISMRMRD

git clone https://github.com/ismrmrd/ismrmrd
cd ismrmrd/
mkdir build
cd build
cmake ../
make
sudo make install

4 Install AVIONIC recon lib

git clone https://github.com/IMTtugraz/AVIONIC.git
cd AVIONIC/CUDA
mkdir build
cd build
cmake .. -DGPUNUFFT_ROOT_DIR=/path/to/gpuNUFFT
make -j 

5 Add binary to PATH (bash)

in ~/.bashrc add:
export PATH=/path/to/AVIONIC/bin/:${PATH} 

Doc

In order to generate the code documentation, run

make doc

and open the file doc/html/index.html.

Display help

avionic --help

Example reconstruction

1 Cartesian

wget ftp://ftp.tugraz.at/outgoing/avionic_testfiles/cine_tpat8_sedona.h5
mkdir ./recon_tpat/
avionic -r cine_tpat_8_sedona.h5 -a ./recon_tpat/recon.dcm

2 Radial

wget ftp://ftp.tugraz.at/outgoing/avionic_testfiles/cine_rad_24_sedona.h5
mkdir ./recon_rad/
avionic -r cine_rad_24_sedona.h5 -a -n ./recon_rad/recon.dcm