Coil combination method using SVD and ESPIRiT

This script can be used as a command-line tool to combine individual coil data into a single image using the SVD-ESPIRiT coil combination technique.

Requirements

The following software should be installed prior to using the script:

• Python 2.7 or Python 3.x (tested on Python 3.5)
• BART [https://mrirecon.github.io/bart/]
• nibabel Python package
• numpy Python package
• blessed or blessings Python package (optional)

Installation

• download the script
• (optional) for your convenience it should be placed inside a directory where executables are usually located, e.g. ~/.local/bin
• (optional) make sure that the directory is in your PATH

• (optional) make sure that the script is executable, e.g. with

  chmod a+x coil_combination_svd_espirit.py

• run the script! :-) (see Usage for details).

• latest / development versions of the script could be found at: https://bitbucket.org/norok2/scripts

Usage

The script requires two NIfTI images (magnitude and phase) containing 4D volumes where the first three dimensions are for spatial information and the individual channels are through the fourth dimension.

Depending on your setup, the script runs with:

python coil_combination_svd_espirit.py

or:

coil_combination_svd_espirit.py

or:

./coil_combination_svd_espirit.py

Additional explanation, including for the accepted arguments, will be output by issuing:

coil_combination_svd_espirit.py --help

(or equivalent).

Copyright

Copyright (C) 2016 Riccardo Metere <metere@cbs.mpg.de>

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Acknowledgements

This script is loosely based on Berkin Bilgic's toolbox http://martinos.org/~berkin/SVD_ESPIRiT_Coil_Combine_Toolbox_v2.zip. Special thanks to Ahmad Seif Kanaan for his contributions.

References

1. Metere, R., Kanaan, A.S., Bilgic, B., Schlumm, T., Möller, H.E., 2017. Effects of the coil combination algorithm on quantitative susceptibility mapping. Under Review.
2. Chatnuntawech, I., McDaniel, P., Cauley, S.F., Gagoski, B.A., Langkammer, C., Martin, A., Grant, P.E., Wald, L.L., Setsompop, K., Adalsteinsson, E., Bilgic, B., 2016. Single-step quantitative susceptibility mapping with variational penalties. NMR Biomed. n/a-n/a. doi:10.1002/nbm.3570
3. Bilgic, B., Polimeni, J.R., Wald, L.L., Setsompop, K., 2016. Automated tissue phase and QSM estimation from multichannel data, in: Proceedings of the ISMRM 24th Annual Meeting & Exhibition. Presented at the 24th Annual Meeting & Exhibition of the International Society for Magnetic Resonance in Medicine, Singapore.
4. Uecker, M., Lustig, M., 2016. Estimating absolute-phase maps using ESPIRiT and virtual conjugate coils. Magn. Reson. Med. n/a-n/a. doi:10.1002/mrm.26191