Segmentator
Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed and tested using ultra-high field magnetic resonance imaging (MRI) brain data.
The goal is to provide a complementary tool to the already available brain tissue segmentation methods (to the best of our knowledge) in other software packages (FSL, CBS-Tools, ITK-SNAP, Freesurfer, SPM, Brainvoyager, etc.).
Citation:
- Our paper can be accessed from this link.
- Released versions of this package can be cited by using our Zenodo DOI.
Core dependencies
Python 3.6 or Python 2.7 (compatible with both).
| Package | Tested version |
|---|---|
| matplotlib | 3.1.1 |
| NumPy | 1.22.0 |
| NiBabel | 2.5.1 |
| SciPy | 1.3.1 |
| Compoda | 0.3.5 |
Installation & Quick Start
- Download the latest release and unzip it.
- Change directory in your command line:
cd /path/to/segmentator - Install the requirements by running the following command:
pip install -r requirements.txt - Install Segmentator:
python setup.py install - Simply call segmentator with a nifti file:
segmentator /path/to/file.nii.gz - Or see the help for available options:
segmentator --help
Check out our wiki for further details such as GUI controls, alternative installation methods and more...
Support
Please use GitHub issues for questions, bug reports or feature requests.
License
Copyright © 2019, Omer Faruk Gulban and Marian Schneider. This project is licensed under BSD-3-Clause.
References
This application is mainly based on the following work:
- Kniss, J., Kindlmann, G., & Hansen, C. D. (2005). Multidimensional transfer functions for volume rendering. Visualization Handbook, 189–209. http://doi.org/10.1016/B978-012387582-2/50011-3
Acknowledgements
Since early 2020, development and maintenance of this project is being actively supported by Brain Innovation as the main developer (Omer Faruk Gulban) works there.