stitching is a simple command line tool to compose whole-body scans acquired over multiple stations.
@article{lavdas2019machine,
title={Machine learning in whole-body MRI: experiences and challenges from an applied study using multicentre data},
author={Lavdas I and Glocker B and Rueckert D and Taylor SA and Aboagye EO and Rockall AG},
journal={Clinical Radiology},
year={2019},
}
If you make use of stitching, it would be great if you cite this paper in any resulting publications.
stitching 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>.
stitching 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 ./stitching -h to see a list of command line arguments.