selfgated_noncartesian_reconstruction

Self-gated 3D Stack-of-Spirals Ultra-Short Echo-Time Pulmonary imaging at 0.55T

Installation

This toolbox was designed to be used with GPUs and cannot be installed without cuda support. This release was tested with CUDA 11.0 and above but may work with older releases of cuda.

Install Pre-requisites:

mkdir mrprogs && cd mrprogs

Install Ubuntu toolboxes:

sudo apt install --no-install-recommends --no-install-suggests --yes apt-utils build-essential cmake cpio cython3 gcc-multilib git-core h5utils hdf5-tools jove jq libace-dev libarmadillo-dev libatlas-base-dev libcrypto++-dev libfftw3-dev libfreetype6-dev libgtest-dev libhdf5-serial-dev liblapack-dev liblapacke-dev libopenblas-base libopenblas-dev libplplot-dev libpugixml-dev libxml2-dev libxslt-dev librocksdb-dev net-tools ninja-build pkg-config python3-dev python3-pip software-properties-common supervisor wget googletest googletest-tools librange-v3-dev nlohmann-json3-dev libboost-all-dev

Install zfp:

git -c advice.detachedHead=false clone --branch 0.5.5 --single-branch https://github.com/LLNL/zfp.git && cd zfp && mkdir build && cd build && cmake ../ -DCMAKE_INSTALL_PREFIX=/home/$USER/local/ && cmake --build . --config Release --parallel $(nproc) && cmake --install . && cd ../../ && rm -rf zfp

Install Gadgetron:

git clone https://github.com/ahsanjav/gadgetron.git && cd gadgetron && git checkout WIPDCF && mkdir build && mkdir /home/$USER/local && cd build && cmake ../ -DCMAKE_INSTALL_PREFIX=/home/$USER/local -G Ninja && ninja install && cd ../../

Install Toolbox:

git clone https://github.com/NHLBI-MR/selfgated_noncartesian_reconstruction.git && cd selfgated_noncartesian_reconstruction && mkdir build && cd build && cmake ../ -DCMAKE_INSTALL_PREFIX=/home/$USER/local -G Ninja && ninja install