checkout and build gadgetron from https://github.com/gadgetron/gadgetron

update the environment using the environment.yml file in this repository

mamba env update -f environment.yml

build the code using

mkdir build && cd build && cmake ../ -GNinja -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} -DC_PREFIX_PATH=${CONDA_PREFIX} -DUSE_CUDA=ON -DUSE_MKL=ON

once built, the package can be used with gadgetron using the config xml files provided with this repository.

the docker image can be pulled using the following command:

docker pull gadgetronnhlbi/ubuntu_2004_cuda117_public_icomoco:built_rt

This image can be deployed with:

docker run --gpus all --name=deploy_rt -ti -p 9063:9002 --volume=[LOCAL_DATA_FOLDER]:/opt/data --restart unless-stopped --detach gadgetronnhlbi/ubuntu_2004_cuda117_public_icomoco:built_rt

where the local data folder is the path to a folder containing raw data that can be used for testing the reconstruction.

once the docker container is running start a bash terminal inside the container using:

docker exec -ti deploy_rt bash

then you can simply navigate to /opt/data/ and test the code using:

gadgetron_ismrmrd_client -p 9002 -f DATA_FILE -c imoco_recon.xml -o OUTPUT_FILENAME.h5

in another terminal session you can monitor the logs from the container using docker logs -f deploy_rt

Please note that if you are using the gadgetron_ismrmrd_client from outside the container then you may need to specify the server address with -a SERVER_ADDRESS and the port -p 9063

The test data can be downloaded from zenodo: https://doi.org/10.5281/zenodo.10456573