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Bruker2nifti

Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format - Published in JOSS (2017)

https://github.com/sebastianof/bruker2nifti

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

Medical image format converter: from raw Bruker ParaVision to nifti.

Basic Info
  • Host: GitHub
  • Owner: SebastianoF
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.48 MB
Statistics
  • Stars: 31
  • Watchers: 5
  • Forks: 21
  • Open Issues: 7
  • Releases: 5
Created almost 9 years ago · Last pushed about 2 years ago
Metadata Files
Readme Authors

README.md

status CircleCI coverage PyPI version

Bruker2nifti

Bruker2nifti is an open source medical image format converter from raw Bruker ParaVision to NifTi, without any intermediate step through the DICOM standard formats.

Bruker2nifti is a pip-installable pure Python tool provided with a Graphical User Interface and a Command Line Utility to access the conversion method.

Before Getting Started

Since the release of ParaVision360v1.1, a NifTi format converter is natively embedded and would provide the long sought standard. Please consider this option before starting with bruker2nifti.

Getting Started

Accessing only the GUI with no Python knowledge required

gui_example

API documentation, additional notes, examples and list of Bruker converter

Code Testing

Support and contributions

Please see the contribution guideline for bugs report, feature requests and code style.

Copyright, Licence and How to Cite

BibTeX entry: @article{ferraris2017bruker2nifti, title={{Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format}}, author={Ferraris, Sebastiano and Shakir, Ismail Dzhoshkun and Van Der Merwe, Johannes and Gsell, Willy and Deprest, Jan and Vercauteren, Tom}, journal={Journal Of Open Source Software}, volume={2}, number={16}, pages={354}, year={2017}, publisher={Journal Of Open Source Software} }

Acknowledgements

  • This repository is developed within the GIFT-surg research project.
  • Funding sources and authors list can be found in the JOSS submission paper.
  • Thanks to Bernard Siow (Centre for Advanced Biomedical Imaging, University College London), Chris Rorden (McCausland Center for Brain Imaging, University of South Carolina) and Matthew Brett (Berkeley Brain Imaging Center).

Owner

  • Name: Sebastiano Ferraris
  • Login: SebastianoF
  • Kind: user
  • Location: London

Data Scientist @ kpler.com

JOSS Publication

Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format
Published
August 27, 2017
DOI
Volume 2, Issue 16, Page 354
Authors
Sebastiano Ferraris ORCID
Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK
Dzhoshkun Ismail Shakir ORCID
Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK
Johannes Van Der Merwe ORCID
Department of Development and Regeneration, Organ System Cluster, Group Biomedical Sciences, KU Leuven, Belgium.
Willy Gsell ORCID
Biomedical MRI, Department of Imaging and Pathology, KU Leuven, Belgium.
Jan Deprest ORCID
Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK, Department of Development and Regeneration, Organ System Cluster, Group Biomedical Sciences, KU Leuven, Belgium., Wellcome/EPSRC Centre for Interventional and Surgical Sciences, University College London, UK.
Tom Vercauteren ORCID
Translational Imaging Group, Centre for Medical Image Computing (CMIC), Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London, WC1E 6BT, UK, Department of Development and Regeneration, Organ System Cluster, Group Biomedical Sciences, KU Leuven, Belgium., Wellcome/EPSRC Centre for Interventional and Surgical Sciences, University College London, UK.
Editor
Kevin M. Moerman ORCID
Tags
Medical Imaging Bruker Nifti Format converter
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Papers & Mentions

Total mentions: 1

Sammba-MRI: A Library for Processing SmAll-MaMmal BrAin MRI Data in Python
Last synced: 4 months ago

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 305
  • Total Committers: 6
  • Avg Commits per committer: 50.833
  • Development Distribution Score (DDS): 0.052
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Sebastiano Ferraris s****s@g****m 289
Jath Palasubramaniam j****a@g****m 6
sebastiano s****o@t****t 5
Riccardo De Feo 3****s 2
Matthew Brett m****t@g****m 2
Gabriel A. Devenyi g****i@g****m 1
Committer Domains (Top 20 + Academic)
thoughtmachine.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 60
  • Total pull requests: 11
  • Average time to close issues: 30 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 15
  • Total pull request authors: 7
  • Average comments per issue: 3.7
  • Average comments per pull request: 1.91
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • SebastianoF (14)
  • dzhoshkun (13)
  • gdevenyi (10)
  • rougier (7)
  • r03ert0 (4)
  • neurolabusc (2)
  • mediumspiny (2)
  • emicotti (1)
  • TheChymera (1)
  • javier-allende (1)
  • amirshamaei (1)
  • hookeba (1)
  • mpompilus (1)
  • cecilyen (1)
  • demianw (1)
Pull Request Authors
  • jathpala (3)
  • SebastianoF (2)
  • Hierakonpolis (2)
  • matthew-brett (1)
  • TheChymera (1)
  • r03ert0 (1)
  • gdevenyi (1)
Top Labels
Issue Labels
help wanted (4) question (2) wontfix (2) for non experts (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 339 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 10
  • Total maintainers: 1
pypi.org: bruker2nifti

From raw Bruker to nifti, home-made converter.

  • Versions: 10
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 339 Last month
Rankings
Dependent packages count: 4.7%
Forks count: 8.7%
Stargazers count: 12.0%
Average: 14.3%
Dependent repos count: 21.7%
Downloads: 24.4%
Maintainers (1)
SebastianoF
Last synced: 6 months ago

Dependencies

Pipfile pypi
  • pytest * develop
  • nibabel >=2.1.0
  • numpy >=1.12.1
requirements-dev.txt pypi
  • mock ==3.0.5 development
  • pre-commit ==1.21.0 development
  • pytest >=4.6.2 development
requirements.txt pypi
  • nibabel >=2.1.0
  • numpy >=1.12.1
  • setuptools >=30.1.0
setup.py pypi