README.md

Example code to reconstruct and retrospectively correct for motion.

To be used with data acquired with the 3D radial Multi-Echo Spin echo sequence.

One example dataset with and without deliberate motion is provided in ISMRMRD format and available at: 10.5281/zenodo.10908742. Reconstructed maps are also provided.

The example code can be used to reconstruct the motion corrupted dataset with and without motion correction.

The related paper "Whole-brain T2 mapping with radial sampling and retrospective motion correction at 3T" is currently under submission.

Nadege Corbin, Centre de Resonance Magnetique des Systemes Biologiques UMR 5536 CNRS/Bordeaux University 2024.04.16

Requirements

This reconstruction code requires multiple softwares and toolbox

• MATLAB (tested with R2019b)
• Gadgetron (https://github.com/gadgetron/gadgetron)
• SPM (https://github.com/spm/)
• EPG-X (https://github.com/mriphysics/EPG-X)
• Anima (https://github.com/Inria-Empenn/Anima-Public)
• sdc3_nrz_11aug (https://github.com/ISMRM/mri_unbound/tree/master/sdc3)

Step 1: copy files in the right place

• create the folder [path to gadgetron]/+gadgetron/+custom/+MESE_RAD

• copy handle_connection_MESE_RAD_shared.m there

• if it does not exist, create the folder [path to gadgetron]/+gadgetron/+custom/+utils

• copy apply_traj_kdata_clean.m there

• copy unif_traj.m there

• copy write_basis_shared.m there

• copy MESE_RAD_shared_6ch.xml MESE_RAD_shared_12ch.xml into /usr/local/share/gadgetron/config

Step 2: Update path

update the path to SPM, EPG-X and sdc3_nrz_11aug in the matlab file write_param.m

Step 3: start gadgetron

Open a terminal go to the "Reco_MESE_RAD" folder start gadgetron with the command: gadgetron -p 9002

Open a second terminal: go to the "Reco_MESE_RAD" folder run example script with the following command : ./run_example.sh [h5_file_name] [output_folder]