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QUIT

QUIT: QUantitative Imaging Tools - Published in JOSS (2018)

https://github.com/spinicist/quit

Science Score: 95.0%

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
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    1 of 14 committers (7.1%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords from Contributors

blackhole gravitational-lenses meshes mri pypi annotations simulations hydrology stellar exoplanets

Scientific Fields

Medicine Life Sciences - 84% confidence
Neuroscience Life Sciences - 84% confidence
Last synced: 4 months ago · JSON representation

Repository

A set of tools for processing Quantitative MR Images

Basic Info
  • Host: GitHub
  • Owner: spinicist
  • License: mpl-2.0
  • Language: C++
  • Default Branch: master
  • Size: 4.53 MB
Statistics
  • Stars: 64
  • Watchers: 10
  • Forks: 21
  • Open Issues: 3
  • Releases: 8
Created over 10 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

Logo

Build DOI DOI Binder

Credit / Blame / Contact - Tobias Wood - tobias.wood@kcl.ac.uk

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

If you find the tools useful the author would love to hear from you.

Brief Description

A collection of programs for processing quantitative MRI data, originally DESPOT but now a wider variety of techniques.

Thanks

Many thanks to Samuel Hurley, Erika Raven, Anna Combes, Amy McDowell and Sjoerd Vos.

Documentation

Documentation is available at http://quit.readthedocs.io (and the in Docs folder in .rst format).

Installation

Executable

Pre-compiled executables are provided for Linux and Mac OS X in a .tar.gz archive from http://github.com/spinicist/QUIT/releases. Download the archive and extract it with tar -xzf qi-platform.tar.gz. Then, move the resulting qi file to somewhere on your $PATH, for instance /usr/local/bin. That's it.

  • MacOS Catalina or higher users should use curl to download the binary, i.e. type curl -L https://github.com/spinicist/QUIT/releases/download/v3.0/qi-macos.tar.gz This is because Safari now sets the quarantine attribute of all downloads, which prevents them being run as the binary is unsigned. It is possible to remove the quarantine flag with xattr, but downloading with curl is more straightforward.
  • The Linux executable is compiled on Ubuntu 22.04 with GLIBC version 2.35 and a statically linked libc++. This means it will hopefully run on most modern Linux distributions. Let me know if it doesn't.

For instructions on how to compile from source, please see the developer page in the documentation.

Python

QUIT now comes with nipype wrappers. Install with pip install qipype.

Usage

QUIT comes as a single executable file with multiple commands, similar to git or bart. Type qi to see a list of all the available commands. The majority of commands require an input 4D Nifti file containing the image data to fit, and a .json file containing the sequence parameters (e.g. TR). See examples for each command at https://quit.readthedocs.io.

An example iPython notebook is available here in a separate repo https://github.com/spinicist/qipype-binder. Workflows for CEST and MPM are provided in qipype.workflows.

Getting Help

If you can't find an answer to a problem in the documentation or help strings, you can open an issue, or find the developer on Twitter (@spinicist).

Owner

  • Name: Tobias Wood
  • Login: spinicist
  • Kind: user
  • Company: King's College London

JOSS Publication

QUIT: QUantitative Imaging Tools
Published
June 21, 2018
DOI
Volume 3, Issue 26, Page 656
Authors
Tobias C. Wood ORCID
Department of Neuroimaging, King's College London
Editor
Christopher R. Madan ORCID
Tags
neuroimaging mri cpp quantitative imaging
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 6
  • Push event: 17
  • Fork event: 1
  • Create event: 1
Last Year
  • Watch event: 6
  • Push event: 17
  • Fork event: 1
  • Create event: 1

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 1,243
  • Total Committers: 14
  • Avg Commits per committer: 88.786
  • Development Distribution Score (DDS): 0.035
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Tobias Wood t****s@s****k 1,199
Tobias Wood t****s@m****m 17
Jeremie Fouquet j****2@g****m 9
Emil Ljungberg l****l@g****m 4
Tobias Wood t****s@F****x 3
Ricardo Rios-Carrillo r****r@u****a 2
Emil Ljungberg e****g@k****k 2
dependabot[bot] 4****] 1
Nir Solomon n****4@g****m 1
Mathieu Boudreau e****0@g****m 1
Lewis Cowles l****s@m****m 1
Arfon Smith a****n 1
Tobias Wood T****s@B****l 1
NeuroDebian User b****n@n****n 1
Committer Domains (Top 20 + Academic)
me.com: 1 kcl.ac.uk: 1 uwo.ca: 1 fenchurch.fritz.box: 1 mi3.com: 1 spinicist.org.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 30
  • Total pull requests: 16
  • Average time to close issues: 2 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 19
  • Total pull request authors: 10
  • Average comments per issue: 3.23
  • Average comments per pull request: 1.31
  • Merged pull requests: 12
  • 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
  • jeremie-fouquet (3)
  • oesteban (3)
  • AndrewLawrence (2)
  • emilljungberg (2)
  • andersonwinkler (2)
  • halfSpinDoctor (2)
  • gdevenyi (2)
  • mathieuboudreau (2)
  • miladseyfi (2)
  • Lewiscowles1986 (1)
  • brycegeeraert (1)
  • RicardoRios46 (1)
  • CarolynMcNabb (1)
  • eugenegkim (1)
  • seareel (1)
Pull Request Authors
  • jeremie-fouquet (6)
  • emilljungberg (5)
  • gdevenyi (2)
  • RicardoRios46 (2)
  • arfon (1)
  • dependabot[bot] (1)
  • mathieuboudreau (1)
  • Lewiscowles1986 (1)
  • em-blue (1)
  • nirso (1)
Top Labels
Issue Labels
Docs (1)
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 8 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 1
pypi.org: qipype

nipype interfaces to QUantitative Imaging Tools

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 8 Last month
Rankings
Forks count: 8.9%
Stargazers count: 9.3%
Dependent packages count: 10.1%
Average: 18.4%
Dependent repos count: 21.6%
Downloads: 42.2%
Maintainers (1)
tcwood
Last synced: 4 months ago

Dependencies

Python/setup.py pypi
  • nibabel >=2.5.1
  • nipype >=1.2.3
docs_requirements.txt pypi
  • mkdocs ==0.17.3
  • python-markdown-math ==0.5
.github/workflows/build.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/create-release v1.0.0 composite
  • actions/download-artifact v1 composite
  • actions/setup-python v1 composite
  • actions/upload-artifact v1 composite
  • actions/upload-release-asset v1.0.1 composite
vcpkg.json vcpkg
  • args *
  • ceres *
  • eigen3 *
  • fmt *
  • itk *
  • nlohmann-json *