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3D MRI data exploration and segmentation tool.
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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.

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

cd /path/to/segmentator
  • Install the requirements by running the following command:
pip install -r requirements.txt
  • Install Segmentator:
python 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:

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