dixonfix is a command line tool to correct fat-water swaps in Dixon MRI. It makes use of graph cut optimization to determine a pixel-wise swap labelling.
@inproceedings{glocker2016correction,
title={Correction of fat-water swaps in Dixon MRI},
author={Glocker, Ben and Konukoglu, Ender and Lavdas, Ioannis and Iglesias, Juan Eugenio and Aboagye, Eric O and Rockall, Andrea G and Rueckert, Daniel},
booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
pages={536--543},
year={2016},
organization={Springer}
}
If you make use of dixonfix, it would be great if you cite this paper in any resulting publications.
dixonfix depends on several third-party libraries:
Eigen is a header-only library and can be simply installed via:
#!bash
$ mkdir 3rdparty
$ cd 3rdparty
$ wget https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz --progress=bar:force:noscroll
$ mkdir eigen
$ tar xf eigen-3.3.7.tar.gz -C eigen --strip-components=1
You can download and install ITK in the same 3rdparty folder via:
#!bash
$ wget https://sourceforge.net/projects/itk/files/itk/5.0/InsightToolkit-5.0.0.tar.gz
$ tar xvf InsightToolkit-5.0.0.tar.gz
$ cd InsightToolkit-5.0.0
$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=../../itk ..
$ make -j4
$ make install
Alternatively, you can check out these ITK install instructions.
You can install Boost and TBB via apt-get:
#!bash
$ sudo apt-get install libboost-all-dev
Note, you might have to specify a specific version via apt-get install <package>=<version>.
dixonfix comes with a CMake configuration file. From the top folder where CMakeLists.txt is located (same as this README), do the following to build all internal libraries and executables:
#!bash
$ mkdir build
$ cd build
$ export THIRD_PARTY_DIR=<folder_containing_eigen_and_itk>
$ cmake ..
$ make -j4
Run ./dixonfix -h to see a list of command line arguments.