stitching

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.

Dependencies

stitching depends on several third-party libraries:

• Eigen
• Boost (tested up to v1.58)
• ITK (tested up to v4.13.2)

Build instructions

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

Usage

Run ./stitching -h to see a list of command line arguments.