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.
Installation & Quick Start
- Download the latest release and unzip it.
- Change directory in your command line:
- 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:
- Or see the help for available options:
Please use GitHub issues for questions, bug reports or feature requests.
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