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 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.
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>
Arguments: <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. Options: -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 : multi-channel registration, modelling of hyper and hypo-intensities.
- v1.1: initial code release, method described in .
Citation and acknowledgements
In case you found Draw-EM useful please give appropriate credit to the software.
- A. Makropoulos et al. "Automatic whole brain MRI segmentation of the developing neonatal brain", IEEE TMI, 2014
- A. Makropoulos, E. C. Robinson et al. "The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction", NeuroImage, 2018