Developing brain Region Annotation With Expectation-Maximization
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README.md

README.md

Draw-EM Segmentation Software

Draw-EM (Developing brain Region Annotation With Expectation-Maximization) is a package of MIRTK developed by Antonios Makropoulos and the BioMedIA research group. It provides a collection of command-line tools as well as pipelines for the segmentation of developing brain MR images.

Installation

Draw-EM is part of MIRTK. In order to compile it as part of MIRTK you need to do the following steps:

  • download (clone) Draw-EM inside the Packages folder of your MIRTK directory
  • enable compile of the package by setting the CMake flag "MODULE_DrawEM" of MIRTK to "ON" (using cmake or ccmake)
  • build MIRTK

See the installation instructions for a step-by-step guide on how to install MIRTK.

The segmentation pipeline further requires the following:

  • FSL installed
  • The atlases required by Draw-EM need to be downloaded from here and extracted inside the Draw-EM directory.
  • The N4 bias field correction from ITK is included in the ThirdParty/ITK folder. If the executable does not work, you will need to compile ITK and replace the ThirdParty/ITK/N4 binary with the N4BiasFieldCorrectionImageFilter binary

Run

The segmentation pipeline can be run with the following script:

pipelines/neonatal-pipeline-v1.1.sh

The script requires the T2 image and the age at scan of the subject to be segmented (as first and second argument respectively). Run the script without arguments for a detailed list of options.

License

Draw-EM is distributed under the terms of the Apache License Version 2. See the accompanying license file for details. The license enables usage of Draw-EM in both commercial and non-commercial applications, without restrictions on the licensing applied to the combined work.

Draw-EM uses third-party software, namely the "ITK: The Insight Toolkit for Segmentation and Registration". ITK is distributed under the Apache License Version 2. Specifically, the N4 bias field correction by Tustison et al. is included (http://www.insight-journal.org/browse/publication/640). The covered file (N4) and license (LICENSE) can be found in ThirdParty/ITK.

Citation and acknowledgements

In case you found Draw-EM useful please give appropriate credit to the software.

Publication:

A. Makropoulos et al. Automatic whole brain MRI segmentation of the developing neonatal brain, IEEE TMI, 2014