Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.6%) to scientific vocabulary
Keywords
Repository
3D MRI data exploration and segmentation tool.
Basic Info
- Host: GitHub
- Owner: ofgulban
- License: bsd-3-clause
- Language: Python
- Default Branch: master
- Homepage: https://github.com/ofgulban/segmentator/wiki
- Size: 3.89 MB
Statistics
- Stars: 75
- Watchers: 11
- Forks: 14
- Open Issues: 13
- Releases: 9
Topics
Metadata Files
README.md
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.
Owner
- Name: Omer Faruk Gulban
- Login: ofgulban
- Kind: user
- Location: Maastricht, The Netherlands
- Company: Brain Innovation
- Website: https://orcid.org/0000-0001-7761-3727
- Twitter: ofgulban
- Repositories: 38
- Profile: https://github.com/ofgulban
I have received my PhD in 2020 from Maastricht University with my thesis titled "Imaging the human auditory system at ultra-high magnetic fields".
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Gulban
given-names: Omer Faruk
orcid: https://orcid.org/0000-0001-7761-3727
- family-names: Schneider
given-names: Marian
orcid: http://orcid.org/0000-0003-3192-5316
- family-names: Marquardt
given-names: Ingo
orcid: http://orcid.org/0000-0001-5178-9951
- family-names: Haast
given-names: Roy
orcid: http://orcid.org/0000-0001-8543-2467
- family-names: De Martino
given-names: Federico
orcid: https://orcid.org/0000-0002-0352-0648
title: "A scalable method to improve gray matter segmentation at ultra high field MRI"
version: 1.6.0
doi: https://doi.org/10.1371/journal.pone.0198335
date-released: 2019-09-26
GitHub Events
Total
- Watch event: 1
- Fork event: 1
Last Year
- Watch event: 1
- Fork event: 1
Dependencies
- compoda ==0.3.5
- matplotlib ==3.1.1
- nibabel ==2.5.1
- numpy ==1.22.0
- pytest-cov ==2.7.1
- scipy ==1.3.1
- compoda >=0.3
- matplotlib >=3.1
- numpy >=1.17
- scipy >=1.3