|
1 | | -Draw-EM Segmentation Software |
2 | | -========================================== |
| 1 | +# Draw-EM Segmentation Software |
| 2 | + |
| 3 | + |
3 | 4 |
|
4 | 5 | Draw-EM (Developing brain Region Annotation With Expectation-Maximization) is a package of [MIRTK](https://github.com/BioMedIA/MIRTK) developed by Antonios Makropoulos and the [BioMedIA](https://biomedia.doc.ic.ac.uk/) research group. |
5 | | -It provides a collection of command-line tools as well as pipelines for the segmentation of developing brain MR images. |
| 6 | +It provides a collection of command-line tools and pipelines for the segmentation of developing brain MR images. |
| 7 | + |
| 8 | +Draw-EM is used as part of the [dHCP structural pipeline](https://github.com/BioMedIA/dhcp-structural-pipeline) for the structural analysis (segmentation and surface extraction) of the neonatal brain. |
| 9 | + |
| 10 | + |
| 11 | +## Dependencies |
| 12 | +### FSL |
6 | 13 |
|
| 14 | +The segmentation pipeline uses |
| 15 | +[FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL). |
| 16 | +See the [installation instructions](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation) for FSL. |
7 | 17 |
|
8 | | -Installation |
9 | | ------------- |
| 18 | + |
| 19 | +## Installation |
10 | 20 |
|
11 | 21 | Draw-EM is part of MIRTK. |
12 | | -In order to compile it as part of MIRTK you need to do the following steps: |
13 | | -- download (clone) Draw-EM inside the Packages folder of your MIRTK directory |
14 | | -- enable compile of the package by setting the CMake flag "MODULE_DrawEM" of MIRTK to "ON" (using cmake or ccmake) |
| 22 | +In order to compile it as part of MIRTK you need to: |
| 23 | +- enable compilation of the package by setting the CMake flag "MODULE_DrawEM" of MIRTK to "ON" (using cmake or ccmake) |
15 | 24 | - build MIRTK |
16 | 25 |
|
17 | 26 | See the [installation instructions](https://mirtk.github.io/install.html) |
18 | 27 | for a step-by-step guide on how to install MIRTK. |
19 | 28 |
|
20 | | -The segmentation pipeline further requires the following: |
21 | | -- [FSL](http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) installed |
22 | | -- The atlases required by Draw-EM need to be downloaded from [here](https://www.doc.ic.ac.uk/~am411/atlases-DrawEM.html) and extracted inside the Draw-EM directory. |
23 | | -- 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 |
24 | | - |
25 | | - |
26 | | -Run |
27 | | ---- |
| 29 | +## Running the pipeline |
28 | 30 |
|
29 | | -The segmentation pipeline can be run with the following script: |
| 31 | +The segmentation pipeline can be run as follows: |
30 | 32 |
|
31 | | -pipelines/neonatal-pipeline-v1.1.sh |
| 33 | +mirtk neonatal-segmentation <subject_T2> <age_at_scan> |
32 | 34 |
|
33 | | -The script requires the T2 image and the age at scan of the subject to be segmented (as first and second argument respectively). |
34 | | -Run the script without arguments for a detailed list of options. |
| 35 | +``` |
| 36 | +Arguments: |
| 37 | + <subject_T2> Nifti Image: The T2 image of the subject to be segmented. |
| 38 | + <age_at_scan> Integer: Subject age in weeks. This is used to select the appropriate template for the initial registration. |
| 39 | + If the age is <28w or >44w, it will be set to 28w or 44w respectively. |
| 40 | +Options: |
| 41 | + -d / -data-dir <directory> The directory used to run the script and output the files. |
| 42 | + -c / -cleanup <0/1> Whether cleanup of temporary files is required (default: 1) |
| 43 | + -p / -save-posteriors <0/1> Whether the structures' posteriors are required (default: 0) |
| 44 | + -t / -threads <number> Number of threads (CPU cores) allowed for the registration to run in parallel (default: 1) |
| 45 | + -v / -verbose <0/1> Whether the script progress is reported (default: 1) |
| 46 | + -h / -help / --help Print usage. |
| 47 | +``` |
35 | 48 |
|
36 | 49 |
|
37 | | -License |
38 | | -------- |
| 50 | +## License |
39 | 51 |
|
40 | 52 | Draw-EM is distributed under the terms of the Apache License Version 2. |
41 | 53 | See the accompanying [license file](LICENSE.txt) for details. The license enables usage of |
42 | 54 | Draw-EM in both commercial and non-commercial applications, without restrictions on the |
43 | 55 | licensing applied to the combined work. |
44 | 56 |
|
45 | | -Draw-EM uses third-party software, namely the "ITK: The Insight Toolkit for Segmentation and Registration". |
46 | | -ITK is distributed under the Apache License Version 2. |
47 | | -Specifically, the N4 bias field correction by Tustison et al. is included (http://www.insight-journal.org/browse/publication/640). |
48 | | -The covered file (N4) and license (LICENSE) can be found in ThirdParty/ITK. |
| 57 | +## Releases |
| 58 | +- v1.2: dHCP segmentation pipeline, method improvements described in [2]: multi-channel registration, modelling of hyper and hypo-intensities. |
| 59 | +- v1.1: initial code release, method described in [1]. |
49 | 60 |
|
50 | 61 |
|
51 | | -Citation and acknowledgements |
52 | | ------------------------------ |
| 62 | +## Citation and acknowledgements |
53 | 63 |
|
54 | 64 | In case you found Draw-EM useful please give appropriate credit to the software. |
55 | 65 |
|
56 | | -Publication: |
| 66 | +Publications: |
57 | 67 |
|
58 | | -A. Makropoulos et al. Automatic whole brain MRI segmentation of the developing neonatal brain, IEEE TMI, 2014 |
| 68 | +1. A. Makropoulos et al. *"Automatic whole brain MRI segmentation of the developing neonatal brain"*, IEEE TMI, 2014 |
| 69 | +2. A. Makropoulos, E. C. Robinson et al. *"The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction"*, NeuroImage, 2018 |
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