PowerGrid

Software for CPU and GPU accelerated iterative magnetic resonance imaging reconstruction. Quickly transate code from MATLAB/Image Reconstruction Toolbox to C++0 code. Implements GPU accelerated non-uniform Fast Fourier Transforms and field correction via two algorithms. Also supports distributed memory computations via MPI for pcSENSE for correction of motion induced phase error as well as low rank reconstructions.

Depedenencies

• Armadillo - Templated Linear Algebra library. Gives us MATLAB like syntax in C++

• ISMRMRD ISMRM Raw Data Format - HDF5 Based data format for Magnetic Resonance Imaging data

• FFTW - Fastest Fourier Transform in the West - Used for CPU implementations of the FFTs used in Gridding.

• SuperLU5 - Library to support advanced matrix decompositions in Armadillo.

Installing PowerGrid on Linux distributions

Note that GPU accelerated recons are only supported on Linux distributions due to limitations in Nvidia-docker only supporting Linux hosts. As docker support for GPUs expands to other platforms, this may change in the future.

Using Docker (Recommended)

• Install NVIDIA proprietary drivers. Instructions vary depending on your Linux distribution.
• Install Docker
• Install Nvidia-docker (Note that nvidia-docker is being phased out as native docker support for GPUs is landing in Docker CE 19.03 and later. For CentOS 7 and Ubuntu 18.04, you are likely to continute to use nvidia-docker for the forseeable future.)

Useful options include -v /Source/On/Host:/Target/On/Container to mount a directory of data and/or code onto the scanner.

docker pull mrfil/powergrid
docker run --runtime=nvidia -it mrfil/powergrid

Installing dependencies on Ubuntu 16.04 (Not recommended - for advanced users only)

Install PGI Community Edition compilers

You can find instructions for installing the PGI compilers with a free (as in beer) license at (https://www.pgroup.com/products/community.htm).

Add needed packages

sudo apt-get -y update && apt-get install -y g++ gcc curl wget libopenblas-dev \
						libarpack2-dev nano wget git libboost-all-dev \
						libhdf5-dev libfftw3-dev

Install Latest CMake

curl -O -J -L http://cmake.org/files/v3.14/cmake-3.14.0-Linux-x86_64.tar.gz
sudo apt-get -y purge cmake
tar -xvf ./cmake-3.14.0-Linux-x86_64.tar.gz
cd ./cmake-3.14.0-Linux-x86_64
cp -r bin /usr/
cp -r doc /usr/share/
cp -r man /usr/share/
cp -r share /usr/

Install SuperLU5

curl -O -J -L crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz
tar xvf superlu_5.2.1.tar.gz
mkdir /root/SuperLU_5.2.1/build
cd /root/SuperLU_5.2.1/build
cmake ../ -DBUILD_SHARED_LIBS=ON
make
sudo make install

Install Armadillo

git clone https://gitlab.com/conradsnicta/armadillo-code
cd armadillo-code
git checkout 9.200.x
mkdir build
cd build
echo $PATH
cmake ../ -DCMAKE_INSTALL_PREFIX=/opt
make
sudo make install
sudo ldconfig

Install ISMRMRD

git clone https://github.com/ismrmrd/ismrmrd.git
cd ismrmrd
git fetch
git checkout tags/v1.4.0
mkdir ./build
cd build
cmake ../ -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_INSTALL_PREFIX=/opt
make
sudo make install

Set up environment variables

export LD_LIBRARY_PATH="/opt/lib:/opt/lib64:${LD_LIBRARY_PATH}"
export LD_LIBRARY_PATH="/opt/PowerGrid/lib:${LD_LIBRARY_PATH}"
export PATH="${PATH}:/opt/PowerGrid/bin"