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.).
- Our paper can be accessed from this link.
- Released versions of this package can be cited by using our Zenodo DOI.
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 |
- 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...
Please use GitHub issues for questions, bug reports or feature requests.
Copyright © 2019, Omer Faruk Gulban and Marian Schneider. This project is licensed under BSD-3-Clause.
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
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.