MRI algorithms for fat-water separation based on chemical shift with B0-correction
Project description
Copyright (c) 2016–2026 Johan Berglund
mri-fatwater is distributed under the terms of the GNU General Public License
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/.
ABOUT
mri-fatwater is a command-line tool for MRI chemical shift based fat-water separation with B0-correction based on QPBO graph cuts . Input paramaters are provided by human readable configuration files. See example configuration files provided with mri-fatwater for details. Input data can be in DICOM format, or MATLAB format according to the ISMRM 2012 challenge. mri-fatwater is written in Python.
⚠️ This repository was previously named fwqpbo.
The repository was renamed for clarity. Existing links remain valid.
HOW TO USE
First install required packages, see dependencies. To use the command-line tool, type
python -m mri_fatwater.cli -h
To use as a Python script, see example file ./scripts/demo.py. The demo reconstructs data from the ISMRM 2012 challenge (data download required).
HOW TO CITE
Berglund J and Skorpil M. Multi-scale graph-cut algorithm for efficient water- fat separation. Magn Reson Med, 78(3):941-949, 2017. [doi: 10.1002/mrm.26479]
DEPENDENCIES
See ./pyproject.toml.
CONTACT INFORMATION
Johan Berglund, Ph.D.
Uppsala University Hospital,
Uppsala, Sweden
johan.berglund@akademiska.se
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