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qMRLab

qMRLab: Quantitative MRI analysis, under one umbrella - Published in JOSS (2020)

https://github.com/qmrlab/qmrlab

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 12 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: arxiv.org, sciencedirect.com, springer.com, wiley.com, frontiersin.org, joss.theoj.org
  • ✓
    Committers with academic emails
    3 of 19 committers (15.8%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

analysis data-simulation magnetic-resonance-imaging magnetization mapping mri qmri quantitative quantitative-mri relaxometry

Scientific Fields

Mathematics Computer Science - 37% confidence
Last synced: 6 months ago · JSON representation

Repository

Quantitative MRI Made Easy with qMRLab: MRI software for data Simulation, analysis and visualization

Basic Info
  • Host: GitHub
  • Owner: qMRLab
  • License: mit
  • Language: MATLAB
  • Default Branch: master
  • Homepage: https://qmrlab.org
  • Size: 412 MB
Statistics
  • Stars: 169
  • Watchers: 24
  • Forks: 60
  • Open Issues: 86
  • Releases: 12
Topics
analysis data-simulation magnetic-resonance-imaging magnetization mapping mri qmri quantitative quantitative-mri relaxometry
Created over 10 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.md

qMRLab

Build Status OCTAVE_CI_TESTS codecov Documentation Status License Website Compile Twitter Follow

hdr

qMRLab is an open-source software for quantitative MR image analysis.

Our main goal is to provide the community with an intuitive tool for data fitting, plotting, simulation and protocol optimization for a myriad of different quantitative models. The modularity of the qMRLab framework makes it easy to add any additional modules and we encourage everyone to contribute their favorite recipe for qMR!

For documentation 📖, visit the Documentation website.

If you are a developer 🛠, please visit the Wiki page.

Please report any bug 🐛 or suggestions 💭 in GitHub.

For interactive tutorials 🎚, blog posts 🖋 and more, you can visit qMRLab portal.

qMRLab is a fork from the initial project qMTLab.

***

FROM SCANNER

Version controlled, fully transparent & vendor-neutral pulse sequences 🌀.

⬇️

Data-driven, container-mediated, platform-agnostic & BIDS compatible workflows 🔀.

⬇️

Reproducible & modern publication 📚 objects.

TO PUBLICATION

 *** ## References **qMRLab** * [Karakuzu et al. *qMRLab: Quantitative MRI analysis, under one umbrella.* Journal of Open Source Software (JOSS) 2020](https://joss.theoj.org/papers/10.21105/joss.02343) * [Karakuzu et al. *The qMRLab workflow: From acquisition to publication.* ISMRM 2019](https://www.ismrm.org/19/program_files/DP23.htm#005) * [Duval et al. *Quantitative MRI made easy with qMRLab.* ISMRM 2018](http://archive.ismrm.org/2018/2288.html) * [Cabana et al. *Quantitative magnetization transfer imaging made easy with qMTLab: Software for data simulation, analysis, and visualization.* Concepts in Magn Reson 2015](https://onlinelibrary.wiley.com/doi/abs/10.1002/cmr.a.21357) **Applications** * [Soustelle et al. *Correlations of quantitative MRI metrics with myelin basic protein (MBP) staining in a murine model of demyelination.* NMR in Biomed 2019](https://onlinelibrary.wiley.com/doi/abs/10.1002/nbm.4116) * [Kim et al. *Rapid framework for quantitative magnetization transfer imaging with interslice magnetization transfer and dictionary‐driven fitting approaches.* Mag Res Med 2019](https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.27850) * [Boudreau et al. *All you need is a browser: eliminating barriers to MRI education with open-source interactive tutorials.* Junior Fellows Symposium: Africa Challenge, ISMRM 2019](https://www.ismrm.org/19/program_files/W06.htm) * [Romero and Sinha. *Magnetization Transfer Saturation Imaging of Human Calf Muscle: Reproducibility and Sensitivity to Regional and Sex Differences.* J Magn Reson Imaging 2019](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmri.26694) * [Michálek et al. *Fast and accurate compensation of signal offset for T2 mapping.* Magn Reson Mater Phy 2019](https://link.springer.com/article/10.1007/s10334-019-00737-3) * [Barbieri et al. *Circumventing the Curse of Dimensionality in Magnetic Resonance Fingerprinting through a Deep Learning Approach.* arXiv:1811.11477](https://arxiv.org/abs/1811.11477) * [Varma et al. *Low duty-cycle pulsed irradiation reduces magnetization transfer and increases the inhomogeneous magnetization transfer effect.* J of Mag Res 2018](https://www.sciencedirect.com/science/article/abs/pii/S1090780718302088) * [Campbell et al. *Promise and pitfalls of g-ratio estimation with MRI.* NeuroImage 2018](https://www.sciencedirect.com/science/article/pii/S1053811917306857) * [Boudreau and Pike. *Sensitivity regularization of the Cramér‐Rao lower bound to minimize B1 nonuniformity effects in quantitative magnetization transfer imaging.* Mag Res Med 2018](https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.27337) * [Mingasson et al. *AxonPacking: an open-source software to simulate arrangements of axons in white matter.* Frontiers in neuroinformatics 2017](https://www.frontiersin.org/articles/10.3389/fninf.2017.00005/full) **Interactive Tutorials** * [Boudreau M. *New Filtering Module.* qMRLab.org 2019](https://qmrlab.org/2019/08/08/b1filter.html) * [Boudreau M. *Relaxometry Series: MP2RAGE T1 Mapping.* qMRLab.org 2019](https://qmrlab.org/2019/04/08/T1-mapping-mp2rage.html) * [Boudreau M. *Relaxometry Series: Variable Flip Angle T1 Mapping.* qMRLab.org 2018](https://qmrlab.org/jekyll/2018/12/11/T1-mapping-variable-flip-angle.html) * [Boudreau M. *Relaxometry Series: Inversion Recovery T1 Mapping.* qMRLab.org 2018](https://qmrlab.org/jekyll/2018/10/23/T1-mapping-inversion-recovery.html) **Awards** * Karakuzu A. ISMRM Research Exchange Grant 2020 * Karakuzu A. et al. Quantitative MR Study Group Competition, second place, ISMRM 2019 * Boudreau M. et al. Junior Fellows Symposium Challenge, Africa challenge winner, ISMRM 2019 * Karakuzu A. et al. [Magnetic Moments](https://www.youtube.com/watch?v=67GKiK3iFr0), People's Choice Award, ISMRM 2018 **Sponsored by** * [Institut TransMedTech Montréal (ITMT)](https://www.polymtl.ca/transmedtech/) * [Canadian Open Neuroscience Platform (CONP)](https://conp.ca/) * [International Society of Magnetic Resonance in Medicine (ISMRM)](http://ismrm.org) ## Citation If you use qMRLab in you work, please cite: Karakuzu A., Boudreau M., Duval T.,Boshkovski T., Leppert I.R., Cabana J.F., Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab: Quantitative MRI analysis, under one umbrella doi: 10.21105/joss.02343 [![OSF](https://img.shields.io/badge/DOI-10.21105%2Fjoss.02343-green.svg?style=for-the-badge)](https://doi.org/10.21105/joss.02343) ***

The MIT License (MIT)

Copyright (c) 2016 NeuroPoly, Ecole Polytechnique, Universite de Montreal

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Owner

  • Name: qMRLab
  • Login: qMRLab
  • Kind: organization

NeuroPoly, École Polytechnique, Université de Montréal

JOSS Publication

qMRLab: Quantitative MRI analysis, under one umbrella
Published
September 03, 2020
DOI
Volume 5, Issue 53, Page 2343
Authors
Agah Karakuzu ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada, Montreal Heart Institute, University of Montréal, Montréal, Canada
Mathieu Boudreau ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada, Montreal Heart Institute, University of Montréal, Montréal, Canada
Tanguy Duval ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada
Tommy Boshkovski ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada
Ilana R. Leppert
McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montreal, Canada
Jean-François Cabana ORCID
Chaudière-Appalaches Integrated Health and Social Services Center, Sainte-Marie, Canada
Ian Gagnon ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada
Pascale Beliveau ORCID
Department of radio-oncology, Research Center of the University of Montreal Hospital Center, Montreal, Canada
G. Bruce Pike ORCID
McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montreal, Canada, Departments of Radiology and Clinical Neuroscience, Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
Julien Cohen-Adad ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada, Functional Neuroimaging Unit, CRIUGM, University of Montreal, Montreal, Canada
Nikola Stikov ORCID
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Canada, Montreal Heart Institute, University of Montréal, Montréal, Canada
Editor
Kevin M. Moerman ORCID
Tags
Octave quantitative magnetic resonance imaging mri neuroimaging
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 5
  • Watch event: 10
  • Issue comment event: 13
  • Push event: 6
  • Pull request review comment event: 9
  • Pull request review event: 9
  • Pull request event: 5
  • Fork event: 3
  • Create event: 3
Last Year
  • Issues event: 5
  • Watch event: 10
  • Issue comment event: 13
  • Push event: 6
  • Pull request review comment event: 9
  • Pull request review event: 9
  • Pull request event: 5
  • Fork event: 3
  • Create event: 3

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 707
  • Total Committers: 19
  • Avg Commits per committer: 37.211
  • Development Distribution Score (DDS): 0.468
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Tanguy Duval d****y@g****m 376
Mathieu Boudreau e****0@g****m 82
Ian Gagnon i****7@g****m 68
Agah a****u@g****m 49
Ilana LEPPERT i****a@b****a 40
Pascale Beliveau p****a@g****m 34
jfcabana j****a@o****m 34
Julien Cohen-Adad j****n@p****a 6
Tanguy Duval t****6@t****u 3
TommyBoshkovski b****y@g****m 3
Harris h****i@g****m 2
jvelazquez-reyes 6****s 2
Ilana Leppert i****a@i****l 2
BusraBulut222 8****2 1
Jeff n****o@g****m 1
Pascale Beliveau p****d@k****a 1
Ian Gagnon x****x 1
Andrew William Russo a****7@t****u 1
Kristen Thyng k****g@g****m 1
Committer Domains (Top 20 + Academic)
tecfidera.nmr.mgh.harvard.edu: 2 kirk.neuro.polymtl.ca: 1 polymtl.ca: 1 bic.mni.mcgill.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 57
  • Total pull requests: 50
  • Average time to close issues: 29 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 27
  • Total pull request authors: 11
  • Average comments per issue: 4.12
  • Average comments per pull request: 2.76
  • Merged pull requests: 34
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 6
  • Average time to close issues: 2 days
  • Average time to close pull requests: 5 days
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 2.14
  • Average comments per pull request: 1.33
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mathieuboudreau (13)
  • agahkarakuzu (6)
  • AlexMorello (5)
  • annapbarnes (4)
  • amie-demmans (4)
  • jcohenadad (3)
  • rixez (2)
  • harrisoncbrammell (2)
  • Kamila-Bober (1)
  • linyingyingkarina (1)
  • frankbolton (1)
  • antmoev (1)
  • twu3565 (1)
  • Ricmelis80 (1)
  • caporaleas (1)
Pull Request Authors
  • agahkarakuzu (20)
  • mathieuboudreau (14)
  • jvelazquez-reyes (7)
  • amie-demmans (4)
  • harrisoncbrammell (3)
  • TimmWetzel (2)
  • tanguyduval (1)
  • gabuzi (1)
  • nekohayo (1)
  • kthyng (1)
Top Labels
Issue Labels
bug (4) enhancement (2) Octave (2) priority:high (1) Model:MTSAT (1) discussion needed (1) compatibility (1) interface (1) Matlab (1) docker (1) feature request (1)
Pull Request Labels
feature request (3) bug (3) enhancement (2) JOSS PR (2) documentation (1) Matlab (1) mono_t2 (1) Model:MTV (1)

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 26
proxy.golang.org: github.com/qmrlab/qmrlab
  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/qMRLab/qMRLab
  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

.github/workflows/octaveTests.yml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • codecov/codecov-action v1 composite
  • qmrlab/moxunit-action master composite
Deploy/Docker/CI/Dockerfile docker
  • neurodebian focal build
Deploy/Docker/MCR/Dockerfile docker
  • ubuntu 20.04 build
Deploy/Docker/MINIMAL/Dockerfile docker
  • neurodebian focal build
Deploy/Docker/OCTJN/Dockerfile docker
  • jupyter/base-notebook 016833b15ceb build
Deploy/Docker/OCTJN/requirements.txt pypi
  • dash *
  • dash-renderer *
  • dash_core_components *
  • dash_dangerously_set_inner_html *
  • dash_html_components *
  • flask *
  • octave_kernel *
  • plotly *
  • scipy *
  • sos ==0.17.7
  • sos-bash ==0.12.3
  • sos-javascript ==0.9.12.2
  • sos-julia ==0.9.12.1
  • sos-matlab ==0.9.12.1
  • sos-notebook ==0.17.2
  • sos-python ==0.9.12.1
  • sos-r ==0.9.12.2
  • sos-ruby ==0.9.15.0
  • sos-sas ==0.9.12.3