This implements the 3D extension to the unringing method proposed by Kellner et al. (2016) [1]. This was presented by Thea Bautista at ISMRM 2021 [2].
Note that this is a preview version. Its functionality is in the process of being merged into the mrdegibbs command that currently implements the 2D version in the main MRtrix3 repo.
You first need to have a source installation of the main MRtrix3 repo available. If you don't already, these are the minimum steps required:
git clone https://github.com/mrtrix3/mrtrix3.git
cd mrtrix3
./configure
You can add the -nogui option to the ./configure call to avoid the checks for OpenGL & Qt if you don't intend to compile mrview (or shview).
You can then clone & compile this repo:
git clone https://github.com/jdtournier/mrdegibbs3D
cd mrdegibbs3D/
../build
For the build command above to work, it needs to invoke the main MRtrix3 build script (wherever this may be located) with the mrdegibbs3D repo as the current working directory. See the MRtrix3 documentation on modules for full details.
If everything works as it should, you'll find the degibbs3D executable in the bin/ folder. You can invoke it directly using its full path (e.g. ~/mrtrix3/mrdegibbs3D/bin/degibbs3D), or add it to your PATH.
Note: with the instructions above, you cannot relocate the executable elsewhere since it will need to link to the main MRtrix3 library, and expects to find it in the same relative location as when it was compiled. You can however relocate it if you also ensure the main libmrtrix3.so library can still be found at the same relative path to the executable itself. Alternatively, you can add the -noshared flag to the ./configure call above to avoid the generation of the MRtrix3 library, which will result in a larger executable, but with fewer restrictions on relocation.
- E. Kellner, B. Dhital, V. G. Kiselev, and M. Reisert, ‘Gibbs-ringing artifact removal based on local subvoxel-shifts’, Magnetic Resonance in Medicine, vol. 76, no. 5, pp. 1574–1581, 2016.
- T. Bautista, J. O’Muircheartaigh, J. V. Hajnal, and J.-D. Tournier, ‘Removal of Gibbs ringing artefacts for 3D acquisitions using subvoxel shifts’, in Proc. Intl. Soc. Mag. Reson. Med., online, May 2021, vol. 29, p. 3535.