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.).


Core dependencies

Python 3.6 or Python 2.7 (compatible with both).

Package Tested version
matplotlib 3.1.1
NumPy 1.17.2
NiBabel 2.5.1
SciPy 1.3.1
Compoda 0.3.5

Installation & Quick Start

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:


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.