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fRAT

fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data - Published in JOSS (2023)

https://github.com/elliohow/fmri_roi_analysis_tool

Science Score: 100.0%

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 3 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

brain-imaging fmri fmri-preprocessing fmri-roi-analysis neuroimaging python

Keywords from Contributors

mesh

Scientific Fields

Medicine Life Sciences - 88% confidence
Mathematics Computer Science - 88% confidence
Sociology Social Sciences - 87% confidence
Last synced: 4 months ago · JSON representation ·

Repository

An analysis tool that uses per-voxel statistical maps in conjunction with FSL atlases to create per-region statistical maps. Current usage includes the creation of regional maps of temporal signal to noise ratio.

Basic Info
  • Host: GitHub
  • Owner: elliohow
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 327 MB
Statistics
  • Stars: 13
  • Watchers: 1
  • Forks: 4
  • Open Issues: 0
  • Releases: 3
Topics
brain-imaging fmri fmri-preprocessing fmri-roi-analysis neuroimaging python
Created almost 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

fRAT - fMRI ROI Analysis Tool

status PRs Welcome GitHub license Github release (latest by date) Github issues Documentation

fRAT is an open-source python-based GUI application used to simplify the processing and analysis of fMRI data by converting voxelwise maps into ROI-wise maps. An installation of FSL is required in order to use fRAT.

fRAT is written using Python for MacOS, Linux and WSL2.

Documentation:

Home page

Installation instructions

ROI analysis tutorial

Citation

When using fRAT, please include the following citation:

Howley, E., Francis, S., & Schluppeck, D. (2023). fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data. Journal of Open Source Software, 8(85), 5200. https://doi.org/10.21105/joss.05200

Reporting bugs

To report a bug or suggest a new feature, please go to fRAT's Issues.

For other questions, issues or discussion please go to fRAT's Discussions.

Contributing to the project

If you'd like to contribute to the project please read our contributing guidelines. Please also read through our code of conduct.

Versioning

We use Semantic versioning for versioning. For the versions available, see the tag list for this project.

Licensing

This project uses the Apache 2.0 license. For the text version of the license see here. Prior to version 1.0.0, this project used an MIT license.

Images

Owner

  • Name: Elliot Howley
  • Login: elliohow
  • Kind: user
  • Location: Nottingham, UK
  • Company: University of Nottingham

Cognitive Neuroscience PhD student at University of Nottingham

JOSS Publication

fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data
Published
May 11, 2023
DOI
Volume 8, Issue 85, Page 5200
Authors
Elliot Howley ORCID
School of Psychology, University of Nottingham, Nottingham, United Kingdom
Susan Francis ORCID
Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom, NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
Denis Schluppeck ORCID
School of Psychology, University of Nottingham, Nottingham, United Kingdom
Editor
Marcel Stimberg ORCID
Tags
fMRI Neuroscience Nipype Pipeline
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: "1.2.0"
authors:
- family-names: Howley
  given-names: Elliot
  orcid: "https://orcid.org/0000-0002-3868-2516"
- family-names: Francis
  given-names: Susan
  orcid: "https://orcid.org/0000-0003-0903-7507"
- family-names: Schluppeck
  given-names: Denis
  orcid: "https://orcid.org/0000-0002-0634-7713"
contact:
- family-names: Howley
  given-names: Elliot
  orcid: "https://orcid.org/0000-0002-3868-2516"
doi: 10.5281/zenodo.7877605
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Howley
    given-names: Elliot
    orcid: "https://orcid.org/0000-0002-3868-2516"
  - family-names: Francis
    given-names: Susan
    orcid: "https://orcid.org/0000-0003-0903-7507"
  - family-names: Schluppeck
    given-names: Denis
    orcid: "https://orcid.org/0000-0002-0634-7713"
  date-published: 2023-05-11
  doi: 10.21105/joss.05200
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5200
  title: "fRAT: an interactive, Python-based tool for region-of-interest
    summaries of functional imaging data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05200"
  volume: 8
title: "fRAT: an interactive, Python-based tool for region-of-interest
  summaries of functional imaging data"

GitHub Events

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

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 381
  • Total Committers: 4
  • Avg Commits per committer: 95.25
  • Development Distribution Score (DDS): 0.026
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Elliot Howley e****w@h****m 371
dependabot[bot] 4****] 7
Marcel Stimberg m****g@i****r 2
Denis Schluppeck d****k@g****m 1
Committer Domains (Top 20 + Academic)
inserm.fr: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 13
  • Total pull requests: 25
  • Average time to close issues: 13 days
  • Average time to close pull requests: about 2 months
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 5.85
  • Average comments per pull request: 0.56
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 19
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
  • billbrod (7)
  • ZeitgeberH (5)
  • schluppeck (1)
Pull Request Authors
  • dependabot[bot] (19)
  • elliohow (3)
  • schluppeck (2)
  • mstimberg (1)
Top Labels
Issue Labels
bug (2)
Pull Request Labels
dependencies (19) documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 37 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 37
  • Total maintainers: 1
pypi.org: frat-brain

Application for ROI fMRI data analysis.

  • Versions: 37
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 37 Last month
Rankings
Dependent packages count: 6.6%
Downloads: 8.4%
Average: 16.7%
Forks count: 17.3%
Stargazers count: 20.5%
Dependent repos count: 30.6%
Maintainers (1)
elliohow
Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi
  • Sphinx >=5,<6
  • docutils <0.17
  • sphinx_rtd_theme *
poetry.lock pypi
  • 101 dependencies
pyproject.toml pypi
  • altgraph 0.17.2
  • bootstrapped 0.0.2
  • brotli 1.0.9
  • certifi 2022.12.7
  • chardet 3.0.4
  • charset-normalizer 2.0.12
  • ci-info 0.2.0
  • click 7.1.1
  • contourpy 1.0.7
  • cycler 0.10.0
  • cython 0.29.21
  • dash 1.19.0
  • dash-core-components 1.15.0
  • dash-html-components 1.1.2
  • dash-renderer 1.9.0
  • dash-table 4.11.2
  • dataclasses 0.6
  • decorator 4.4.2
  • descartes 1.1.0
  • dill 0.3.6
  • dominate 2.6.0
  • etelemetry 0.2.2
  • filelock 3.0.12
  • flask 1.1.2
  • flask-compress 1.8.0
  • fonttools 4.38.0
  • fslpy 3.4.0
  • funcsigs 1.0.2
  • future 0.18.2
  • gevent 22.10.2
  • greenlet 2.0.2
  • h5py 3.8.0
  • idna 2.9
  • imageio 2.9.0
  • isodate 0.6.0
  • itsdangerous 1.1.0
  • jinja2 2.11.3
  • joblib 1.2.0
  • kiwisolver 1.4.4
  • looseversion 1.0.1
  • lxml 4.9.2
  • macholib 1.15.2
  • markupsafe 1.1.1
  • matplotlib 3.6.3
  • mizani 0.8.1
  • multiprocess 0.70.14
  • networkx 2.4
  • neurdflib 5.0.1
  • nibabel 3.2.1
  • nilearn 0.9.0
  • nipype 1.8.4
  • numpy 1.22.3
  • packaging 23.0
  • palettable 3.3.0
  • pandas 1.5.3
  • pathos 0.2.6
  • patsy 0.5.3
  • pillow 9.3.0
  • pip-autoremove 0.10.0
  • plotly 4.14.3
  • plotnine 0.10.1
  • pox 0.2.8
  • ppft 1.6.6.2
  • prov 1.5.3
  • pydot 1.4.1
  • pydotplus 2.0.2
  • pyinstaller 4.9
  • pyinstaller-hooks-contrib 2022.2
  • pyparsing 2.4.6
  • python ~3.10
  • python-dateutil 2.8.1
  • pytz 2022.7.1
  • pywavelets 1.4.1
  • rdflib 5.0.0
  • requests 2.27.1
  • retrying 1.3.3
  • scikit-image 0.19.3
  • scikit-learn 1.2.1
  • scipy 1.10.0
  • simplejson 3.17.0
  • six 1.14.0
  • sklearn 0.0
  • statsmodels 0.13.5
  • tabulate 0.8.9
  • tenacity 8.2.0
  • threadpoolctl 2.1.0
  • tifffile 2021.7.30
  • toml 0.10.2
  • traits 6.3.2
  • urllib3 1.26.5
  • werkzeug 1.0.1
  • xlrd 1.2.0
  • xmltodict 0.12.0
  • zope-event 4.5.0
  • zope-interface 5.2.0