iCoMoCo Resontruction in Gadgetron

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.

Alternatively the provided docker image can be used to test the code

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

Dataset

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