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Scan Session Tool

Scan Session Tool: (f)MRI scan session documentation and archiving - Published in JOSS (2024)

https://github.com/fladd/scansessiontool

Science Score: 93.0%

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
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    Committers with academic emails
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    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

(f)MRI scan session documentation and archiving

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 24
Created about 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Scan Session Tool

About

There is an urgent need to improve the reproducibility of (functional) MRI research through transparent reporting, but standardization in this domain is currently lacking. Shared MR images are often only made available after transformation into a derivative data format (e.g. BIDS), and scan session documentation is commonly either manually implemented (e.g. with hand written notes) or neglected entirely.

Scan Session Tool was written to fill this gap, and to be used by neuroscientists, to help them increase transparency and reproducibilty of their MRI research by standardizing scan session documentation and raw data archiving.

Scan Session Tool is a graphical application for documenting (f)MRI scan sessions and automatized data archiving. Information about the scan session itself, used forms and documents, as well as the single measurements can be entered and saved into a protocol file. This information can furthermore be used to copy acquired data (DICOM images as well as optional stimulation protocols and logfiles into a specific hierarchical folder structure for unified archiving purposes, with optional sepcial support for (Turbo-)BrainVoyager.

Installation

Using pipx (recommended)

  1. Make sure Python 3 (>=3.6; with Tkinter) is installed.

  2. Install pipx:

    python3 -m pip install --user pipx python3 -m pipx ensurepath (On Windows you might need to replace python3 with py -3).

  3. Install Scan Session Tool:

    pipx install ScanSessionTool

Using pip

  1. Make sure Python 3 (>=3.6; with Tkinter) is installed.

  2. Install Scan Session Tool:

python3 -m pip install ScanSessionTool (On Windows you might need to replace python3 with py -3).

Usage

Scan Session Tool can be started with the command scansessiontool.

Documentation

The full documentation can be found from within the programme, by clicking on the "?" button, or by selecting "Scan Session Tool Help" from the Help menu, as well as at https://fladd.github.io/ScanSessionTool/.

Automated tests

Core functionality of Scan Session Tool can be tested automatically. To do so, first install all dependencies: python -m pip install -r requirements.txt`

Then, run tests from this directory: python -m unittest -v

Contributing

We very much welcome contributions to Scan Session Tool, and there are multiple ways to contribute. Contributions are always handled transparently through the public GitHub interface.

Bug reports

If you encounter bugs or incorrect/unexpected behaviour of Scan Session Tool, please consider creating an issue here on GitHub for it. You can read more about how to do this here. When reporting issues, make sure to report (1) what you were trying to do, (2) what the expected outcome should have been, (3) what the observed outcome is, and (4) how to replicate this behaviour.

Code contributions

We work with the standard GitHub forking workflow and appreciate code contributions in that way. Individuals that have contributed code will be named with their contributions on this page.

Bug fixes

To implement bug fixes, please 1. fork the main branch of this repository 2. commit your changes (potentially in a new branch) 3. test you changes 4. create a pull request and reference the corresponding GitHub issue, if applicable

New features

Before implementing a new feature, we would encourage you to first discuss the planned feature with us, either in the issue tracker, or GitHub discussions. Once discussed, new features can then be implemented the same way as bug fixes.

Contributors

  • Florian Krause (main developer)
  • Nikos Kogias (co-developer)

Owner

  • Name: Florian Krause
  • Login: fladd
  • Kind: user
  • Location: Nijmegen, The Netherlands

JOSS Publication

Scan Session Tool: (f)MRI scan session documentation and archiving
Published
August 07, 2024
DOI
Volume 9, Issue 100, Page 6126
Authors
Florian Krause ORCID
Donders Institute for Brain, Cognition and Behaviour, RadboudUMC, Nijmegen, The Netherlands
Nikos Kogias ORCID
Donders Institute for Brain, Cognition and Behaviour, RadboudUMC, Nijmegen, The Netherlands
Editor
Kevin M. Moerman ORCID
Tags
neuroscience MRI research documentation data archiving
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GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 204
  • Total Committers: 2
  • Avg Commits per committer: 102.0
  • Development Distribution Score (DDS): 0.044
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Florian Krause s****n@g****m 195
nikoskogias1 n****1@g****m 9

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 9
  • Total pull requests: 9
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 months
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 2.44
  • Average comments per pull request: 0.11
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 1
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
  • jsheunis (9)
Pull Request Authors
  • nikoskogias1 (8)
  • fladd (3)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 10 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 1
pypi.org: scansessiontool

Scan Session Tool - A tool for (f)MRI scan session documentation and data archiving

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 10 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Forks count: 22.6%
Stargazers count: 27.8%
Average: 29.1%
Downloads: 63.2%
Maintainers (1)
fladd
Last synced: 6 months ago

Dependencies

setup.py pypi
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  • pydicom *
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  • actions/setup-python v5 composite
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  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/build_and_deploy_dev.yml actions
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  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
requirements.txt pypi
  • PyYAML *
  • dataintegrityfingerprint *
  • pydicom *