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brkraw

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data

https://github.com/brkraw/brkraw

Science Score: 77.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 13 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords

bids bruker converter dataloader nibabel simpleitk

Keywords from Contributors

closember data-storage git-annex usable brain-imaging fmri fmri-preprocessing neuroimaging mesh sequences
Last synced: 6 months ago · JSON representation ·

Repository

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data

Basic Info
  • Host: GitHub
  • Owner: BrkRaw
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Homepage: https://brkraw.github.io
  • Size: 40 MB
Statistics
  • Stars: 47
  • Watchers: 3
  • Forks: 29
  • Open Issues: 36
  • Releases: 8
Topics
bids bruker converter dataloader nibabel simpleitk
Created almost 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

DOI made-with-python Binder

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data

Version: 0.3.11

Description

The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from Bruker Biospin preclinical MRI scanner. This module is also compatible with the zip compressed data to enable use of the archived data directly.
The module is comprised of four components, including graphical user interface (GUI), command-line tools, high-level and low-level python APIs. - For the GUI, we focused on improving convenience for checking metadata and previewing the reconstructed image. - For the command-line tool, we focused on providing tools for converting, organizing, archiving, and managing data. The command-line tool also provides easy-to-use function to convert large set of raw data into organized structure according to BIDS. - For the high-level python API, we focused on enhancing the accessibility of reconstructed image data with preserved image orientation and metadata for the image analysis. It compatible users' convenient objects type (nibabel or SimpleITK) without the conversion step. - For the low-level python API, we focused on providing a consistent method to access raw Bruker data including parameter and binary files with the python compatible datatype while keeping the sake of simplicity.

Conversion reliability

Robust Orientation We've tested our converter using the sample dataset from Bruker2Nifti_QA and the results showed correct geometry and orientation for all datasets. We are still looking for more datasets showing orientation issue, if you have any shareable dataset, please contact the developer.

Website

For more detail information including installation, usage and examples, please visit our GitPage.

Credits:

Authors
  • SungHo Lee (shlee@unc.edu): main developer
  • Woomi Ban (banwoomi@unc.edu): sub-developer who tested and refined the module structure
  • Jaiden Dumas: proofreading of documents and update contents for the user community.
  • Dr. Gabriel A. Devenyi: The vast contributions to refinement of module functionality and troubleshooting.
  • Yen-Yu Ian Shih (shihy@neurology.unc.edu): technical and academical advisory on this project (as well as funding) ##### Contributors
  • Drs. Chris Rorden and Sebastiano Ferraris: The pioneers related this project who had been inspired the developer through their great tools including dcm2niix and bruker2nifti, as well as their comments to improve this project.
  • Dr. Mikael Naveau: The publisher of bruker2nifti_qa, the set of data to help benchmark testing of Bruker converter.

License:

GNU General Public License v3.0

How to get Support

If you are experiencing any problem or have questions, please report it through Issues

Citing BrkRaw

Lee, Sung-Ho, Ban, Woomi, & Shih, Yen-Yu Ian. (2020, June 4). BrkRaw/bruker: BrkRaw v0.3.3 (Version 0.3.3). Zenodo. http://doi.org/10.5281/zenodo.3877179

BibTeX @software{lee_sung_ho_2020_3907018, author = {Lee, Sung-Ho and Ban, Woomi and Shih, Yen-Yu Ian}, title = {BrkRaw/bruker: BrkRaw v0.3.4}, month = jun, year = 2020, publisher = {Zenodo}, version = {0.3.4}, doi = {10.5281/zenodo.3907018}, url = {https://doi.org/10.5281/zenodo.3907018} }

Owner

  • Name: BrkRaw
  • Login: BrkRaw
  • Kind: organization

A comprehensive tool to access raw Bruker Biospin MRI data

Citation (CITATION.cff) 

cff-version: 1.2.0

title: "brkraw"

version: "0.3.10"

abstract: Bruker PvDataset Loader

message: "If you use this software, please cite it as below."

repository-code: "https://github.com/BrkRaw/brkraw"

identifiers:
  - description: This is the collection of archived snapshots of all releases
    type: doi
    value: "10.5281/zenodo.245546149"

contact:
  - email: shlee@unc.edu
    family-names: SungHo 
    given-names: Lee

authors:
  - email: shlee@unc.edu
    family-names: SungHo 
    given-names: Lee

  - email: banwoomi@unc.edu
    family-names: Woomi  
    given-names: Ban

  - family-names: Dumas 
    given-names: Jaiden

  - family-names: Devenyi 
    given-names: Gabriel A.

  - email: shihy@neurology.unc.edu
    family-names: Yen-Yu
    given-names: Ian Shih

license: GPL-3.0

keywords:
  - bruker
  - data_handler
  - converter
  - administrator_tool
  - brain imaging data structure

GitHub Events

Total
  • Issues event: 5
  • Watch event: 2
  • Issue comment event: 7
  • Pull request event: 1
  • Create event: 1
Last Year
  • Issues event: 5
  • Watch event: 2
  • Issue comment event: 7
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 378
  • Total Committers: 13
  • Avg Commits per committer: 29.077
  • Development Distribution Score (DDS): 0.196
Past Year
  • Commits: 32
  • Committers: 6
  • Avg Commits per committer: 5.333
  • Development Distribution Score (DDS): 0.563
Top Committers
Name Email Commits
SungHo Lee s****e@u****u 304
yc y****t@g****m 32
Remi Gau r****u@h****m 14
Woomi Ban b****i@g****m 11
Jeremie Fouquet j****2@g****m 3
Luis Concha l****a@g****m 3
Jaiden Seongmi Dumas 6****d 3
Michael Hanke m****e@g****m 2
dependabot[bot] 4****] 2
Ricardo Rios 4****6 1
Gabriel A. Devenyi g****i@g****m 1
Joanes Grandjean j****n@r****l 1
Joanes Grandjean 2****b 1
Committer Domains (Top 20 + Academic)
radboudumc.nl: 1 unc.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 105
  • Total pull requests: 81
  • Average time to close issues: 8 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 38
  • Total pull request authors: 14
  • Average comments per issue: 3.36
  • Average comments per pull request: 0.86
  • Merged pull requests: 69
  • Bot issues: 0
  • Bot pull requests: 5
Past Year
  • Issues: 5
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • ycAbout (16)
  • gdevenyi (16)
  • Remi-Gau (8)
  • jeremie-fouquet (7)
  • mih (6)
  • timwahoo (5)
  • araikes (4)
  • dvm-shlee (3)
  • cecilyen (3)
  • grandjeanlab (2)
  • mcraig-ibme (2)
  • TheChymera (2)
  • egarza (2)
  • mschneider1711 (2)
  • hille (1)
Pull Request Authors
  • dvm-shlee (30)
  • ycAbout (9)
  • eugenegkim (9)
  • timwahoo (8)
  • banwoomi (7)
  • jeremie-fouquet (6)
  • dependabot[bot] (5)
  • Remi-Gau (4)
  • mih (2)
  • grandjeanlab (2)
  • lconcha (2)
  • jsmi-d (1)
  • gdevenyi (1)
  • RicardoRios46 (1)
Top Labels
Issue Labels
enhancement (20) bug (10) good first issue (3) documentation (2) Notice (2)
Pull Request Labels
dependencies (5) enhancement (2) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 60 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
pypi.org: brkraw

Bruker PvDataset Loader

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 60 Last month
Rankings
Forks count: 7.7%
Dependent packages count: 10.0%
Stargazers count: 10.8%
Average: 16.1%
Dependent repos count: 21.7%
Downloads: 30.6%
Maintainers (1)
dvm-shlee
Last synced: 7 months ago

Dependencies

Dockerfile docker
  • python 3.7 build
.github/workflows/flake8.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
.github/workflows/test.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
.github/workflows/validation.yml actions
  • actions/checkout v4 composite
  • citation-file-format/cffconvert-github-action 2.0.0 composite
pyproject.toml pypi
  • nibabel >=3.0.2
  • numpy >=1.18.0
  • openpyxl >=3.0.3
  • pandas >=1.0.0
  • pillow >=7.1.1
  • tqdm >=4.45.0
  • xlrd >=1.0.0