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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).

PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5

Installation & Quick Start

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

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.

About

3D MRI data exploration and segmentation tool.

github.com/ofgulban/segmentator/wiki

Topics

2dhistogramsgradient-magnitudemrisegmentation

Resources

Readme
BSD-3-Clause license

Contributing

Contributing
Activity

Stars

76 stars

Watchers

10 watching

Forks

13 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

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GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
Resources
Readme
BSD-3-Clause license
Contributing
Contributing
Activity
Stars
76 stars
Watchers
10 watching
Forks
13 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
Resources
Readme
BSD-3-Clause license
Contributing
Contributing
Activity
Stars
76 stars
Watchers
10 watching
Forks
13 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
Resources
Readme
BSD-3-Clause license
Contributing
Contributing
Activity
Stars
76 stars
Watchers
10 watching
Forks
13 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
Resources
Readme
BSD-3-Clause license
Contributing
Contributing
Activity
Stars
76 stars
Watchers
10 watching
Forks
13 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
Resources
Readme
BSD-3-Clause license
Contributing
Contributing
Activity
Stars
76 stars
Watchers
10 watching
Forks
13 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
Resources
Readme
BSD-3-Clause license
Contributing
Contributing
Activity
Stars
76 stars
Watchers
10 watching
Forks
13 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
GitHub - ofgulban/segmentator: 3D MRI data exploration and segmentation tool. · GitHub
Skip to content
BranchesTags
Repository files navigation
DOI
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).
PackageTested version
matplotlib3.1.1
NumPy1.22.0
NiBabel2.5.1
SciPy1.3.1
Compoda0.3.5
Installation & Quick Start
cd /path/to/segmentator

  • Install the requirements by running the following command:
pip install -r requirements.txt

  • Install Segmentator:
python 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:
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.
About
3D MRI data exploration and segmentation tool.
github.com/ofgulban/segmentator/wiki
Topics
2dhistogramsgradient-magnitudemrisegmentation
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BSD-3-Clause license
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