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Draw-EM Segmentation Software

segmentation image

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 and pipelines for the segmentation of developing brain MR images.

Draw-EM is used as part of the dHCP structural pipeline for the structural analysis (segmentation and surface extraction) of the neonatal brain.



The segmentation pipeline uses FSL. See the installation instructions for FSL.


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

  • enable compilation 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.

Running the pipeline

The segmentation pipeline can be run as follows:

mirtk neonatal-segmentation <subject_T2> <age_at_scan>

  <subject_T2>                  Nifti Image: The T2 image of the subject to be segmented.
  <age_at_scan>                 Integer: Subject age in weeks. This is used to select the appropriate template for the initial registration. 
			        					If the age is <28w or >44w, it will be set to 28w or 44w respectively.
  -d / -data-dir  <directory>   The directory used to run the script and output the files. 
  -c / -cleanup  <0/1>          Whether cleanup of temporary files is required (default: 1)
  -p / -save-posteriors  <0/1>  Whether the structures' posteriors are required (default: 0)
  -t / -threads  <number>       Number of threads (CPU cores) allowed for the registration to run in parallel (default: 1)
  -v / -verbose  <0/1>          Whether the script progress is reported (default: 1)
  -h / -help / --help           Print usage.


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.


  • v1.2.1: Corpus Callosum segmentation improvement
  • v1.2: dHCP segmentation pipeline, method improvements described in [2]: multi-channel registration, modelling of hyper and hypo-intensities.
  • v1.1: initial code release, method described in [1].

Citation and acknowledgements

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


  1. A. Makropoulos et al. "Automatic whole brain MRI segmentation of the developing neonatal brain", IEEE TMI, 2014
  2. A. Makropoulos, E. C. Robinson et al. "The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction", NeuroImage, 2018


Developing brain Region Annotation With Expectation-Maximization




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