[REVIEW]: qMRLab: Quantitative MRI Analysis, under one umbrella

[whedon]

Submitting author: @agahkarakuzu (Agah Karakuzu)
Repository: https://github.com/qMRLab/qMRLab
Version: v.2.4.1
Editor: @Kevin-Mattheus-Moerman
Reviewer: @grlee77, @mfroeling, @62442katieb
Archive: 10.5281/zenodo.4012104

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/2e87644fb8a9e93d48359565c7726f34/status.svg)](https://joss.theoj.org/papers/2e87644fb8a9e93d48359565c7726f34)

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Review checklist for @grlee77

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@agahkarakuzu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @mfroeling

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@agahkarakuzu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @62442katieb

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@agahkarakuzu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @grlee77, @mfroeling, @62442katieb it looks like you're currently assigned to review this paper 🎉.

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[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2343 with the following error:

sh: 0: getcwd() failed: No such file or directory
pandoc: 10.21105.joss.02343.pdf: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF

[whedon]

👉 Check article proof 📄 👈

[Kevin-Mattheus-Moerman]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.21105/joss.00656 may be missing for title: QUIT: QUantitative imaging tools
- https://doi.org/10.1016/b978-012372560-8/50002-4 may be missing for title: Statistical parametric mapping
- https://doi.org/10.1101/343079 may be missing for title: Let’s talk about cardiac T1 mapping
- https://doi.org/10.1016/j.softx.2019.100369 may be missing for title: Total Mapping Toolbox (TOMATO): An open source library for cardiac magnetic resonance parametric mapping
- https://doi.org/10.5210/fm.v3i2.578 may be missing for title: The cathedral and the bazaar

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@grlee77, @mfroeling, @62442katieb this is where the review takes place. Please read the above instructions ☝️ (including suggestions on preventing unwanted GitHub notifications).

You each have a set of checkboxes to guide you through the review process. It would be great if you could review this work in about 2 weeks. Although we can be flexible regarding review time (especially during these challenging times!!!) it would be great if you would let us know if you need more time.

Thanks again for your help!!!! Let the reviewing begin 🎉 🤖 🚀

[Kevin-Mattheus-Moerman]

@grlee77, @mfroeling, @62442katieb thanks again for your help with this review. I see @mfroeling has started. @grlee77, @62442katieb how are you getting on? Let me know if you have questions.

[grlee77]

Hey all, sorry about the delay. I will review this over the next day or so.

[grlee77]

@Kevin-Mattheus-Moerman, can you please resend the invitation?

When I click the link to accept it in the first comment it says it is expired (so I am unable to edit the checklist).

[danielskatz]

@whedon re-invite @grlee77 as reviewer

[whedon]

OK, the reviewer has been re-invited.

@grlee77 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[grlee77]

Re: Contributions and authorship item

Can the authors clarify briefly how authorship criteria were decided? I see that most authors overlap with the repository's significant source code contributors, but I understand contributions can also come in other forms. Two authors I don't see an obvious alias for in the commit history are Drs. Pike and Stikov. Also, there appear to be a few significant contributors (e.g. 30+ commits) who do not appear in the author list (although it is hard to tell for sure based on GitHub handles).

[grlee77]

Re: installation instructions item:

Your documentation for this is good, but it would be nice if you also listed which commercial Matlab toolboxes are required. I saw that for Octave, specific toolboxes were listed.

FWIW, I ran a few of the demos and then typed license('inuse') and saw

image_toolbox
matlab
optimization_toolbox

but I did not run everything, so there may be others as well.

[grlee77]

Please double-check the formatting of the references. For example the first reference (SPM) seems to be incomplete and the Weiskopf et. al. reference has a stray "Citeseer" listed.

[grlee77]

Re: citations:

The authors cite several relevant packages, but one area that does not seem to be represented is for Diffusion MRI. qMRLab does provide DTI, CHARMED and NODDI functionality, so it seems relevant to cite some packages in this area as well. Some common tools for that are free, but not open source, but a few open source ones I am aware of are:

DIPY and DMIPY (Python) (full disclosure: I have been an occasional DIPY contributor)
Camino (Java)
DSI Studio (C++)

Of course, it will not be possible to cite everything, but 1-2 sentences regarding other open-source diffusion processing tools would be nice.

[grlee77]

Regarding the included figure, it is pretty, but I wonder if there is any issue on JOSS's end to publish a figure including logos of other packages like Matlab, Docker, Plotly, etc. When we submitted the SciPy paper (albeit not for JOSS), there were originally various logos in a historical timeline figure, but the editorial team required the removal of any copyrighted logos prior to publication.

Also, when performing this review, I have only reviewed qMRLab itself, but did not evaluate the related projects like qMRFlow, etc. I think it is appropriate to mention these related projects in the text, but I don't think the figure needs to include them. I guess what I am saying is that the figure looks a bit more like an advertisement for the broader software eco-system surrounding qMRLab and should perhaps be a bit more narrowly focused on the quantitative mapping subset described in the publication.

@Kevin-Mattheus-Moerman: can you advise on any potential issues regarding logos on JOSS's end?

[Kevin-Mattheus-Moerman]

Regarding the included figure, it is pretty, but I wonder if there is any issue on JOSS's end to publish a figure including logos of other packages like Matlab, Docker, Plotly, etc. When we submitted the SciPy paper (albeit not for JOSS), there were originally various logos in a historical timeline figure, but the editorial team required the removal of any copyrighted logos prior to publication.

Also, when performing this review, I have only reviewed qMRLab itself, but did not evaluate the related projects like qMRFlow, etc. I think it is appropriate to mention these related projects in the text, but I don't think the figure needs to include them. I guess what I am saying is that the figure looks a bit more like an advertisement for the broader software eco-system surrounding qMRLab and should perhaps be a bit more narrowly focused on the quantitative mapping subset described in the publication.

@Kevin-Mattheus-Moerman: can you advise on any potential issues regarding logos on JOSS's end?

@grlee77 thanks for raising this issue with us. The logos are acceptable.

[Kevin-Mattheus-Moerman]

@agahkarakuzu can you respond to the comments by @grlee77 ?

[62442katieb]

Re: Contributions and authorship item

Can the authors clarify briefly how authorship criteria were decided? I see that most authors overlap with the repository's significant source code contributors, but I understand contributions can also come in other forms. Two authors I don't see an obvious alias for in the commit history are Drs. Pike and Stikov. Also, there appear to be a few significant contributors (e.g. 30+ commits) who do not appear in the author list (although it is hard to tell for sure based on GitHub handles).

I would also like clarification on the authorship decisions. Thanks!

[agahkarakuzu]

@grlee77 @62442katieb

Re: Contributions and authorship item

Two authors I don't see an obvious alias for in the commit history are Drs. Pike and Stikov.

• Bruce Pike and Nikola Stikov (my advisor) are principal investigators of the research labs funding our project

Can the authors clarify briefly how authorship criteria were decided?

• For the authorship, we thought maintainers, active contributors and PIs fit for the authorship. These are the contributors regularly joining our bi-weekly meetings. For clarity, below is a brief breakdown of authorship roles:

  • Agah Karakuzu: Maintainer, improved the qMRLab framework, significant contributions to the codebase, added DevOps and new qMRI models, wrote the manuscript.
  • Mathieu Boudreau: Maintainer, significant contributions to the codebase, added new qMRI models, revised the manuscript
  • Tanguy Duval: Former maintainer, created qMRLab framework based on qMTLab, significant contributions to the codebase, revised the manuscript
  • Tommy Boshkovski: Active contributor, added qMRI models, helped improve documentation, created the web portal, revised the manuscript.
  • Ilana R. Leppert: Active contributor, added qMRI models, revised the manuscript.
  • Bruce Pike: Principal Investigator, contributed funds for the development of the software, revised the manuscript.
  • Julien Cohen-Adad: Principal Investigator, contributions to the codebase, contributed funds for the development of the software, provided valuable insights on software development, revised the manuscript.
  • Nikola Stikov: Principal Investigator, main supervisor of the project and academic supervisor of A.K. and T.B., contributed funds for the development of the software, revised the manuscript

Also, there appear to be a few significant contributors (e.g. 30+ commits) who do not appear in the author list (although it is hard to tell for sure based on GitHub handles).

• I would like to note that later on in the project, we started using squash and merge option to merge the commits into the master. Therefore, at least for this codebase, number of commits is not necessarily an objective measure of the relative code contributions. Nonetheless, we are more than happy to welcome all the contributors as authors if the JOSS policy (@Kevin-Mattheus-Moerman ) requires and/or the reviewers @grlee77 @62442katieb strongly recommend to do so.

Also, when performing this review, I have only reviewed qMRLab itself, but did not evaluate the related projects like qMRFlow, etc. I think it is appropriate to mention these related projects in the text, but I don't think the figure needs to include them.

Thank you @grlee77, I agree with your point. I will update the figure to confine the content to qMRLab codebase only and simplify it.

• The comment will be addressed in the revised manuscript.

The authors cite several relevant packages, but one area that does not seem to be represented is for Diffusion MRI. qMRLab does provide DTI, CHARMED and NODDI functionality, so it seems relevant to cite some packages in this area as well.

Thank you for the suggestion. I agree that including some open source examples from the Diffusion MRI field is relevant.

• The comment will be addressed in the revised manuscript.

• Please double-check the formatting of the references.

• it would be nice if you also listed which commercial Matlab toolboxes are required

Thank you so much @grlee77 for your valuable comments, I will soon address them and make a PR.

[whedon]

OK. v.2.4.1 is the version.

[Kevin-Mattheus-Moerman]

@whedon set 10.5281/zenodo.4012104 as archive

[whedon]

OK. 10.5281/zenodo.4012104 is the archive.

[Kevin-Mattheus-Moerman]

@agahkarakuzu can you amend the title of the ZENODO archived version to match that of the paper? It is currently qMRLab/qMRLab: Release v2.4.1 Zenodo Archive but should be qMRLab: Quantitative MRI analysis, under one umbrella

[agahkarakuzu]

@Kevin-Mattheus-Moerman I fixed the title.

[Kevin-Mattheus-Moerman]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1699

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1699, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

Hi @agahkarakuzu, I am the rotating EIC and I just read through your paper and I see that the capitalization in your references is incorrect. I made changes to your .bib file in this PR.

[mathieuboudreau]

Thanks @kthyng - I approved and merged your PR!

[kthyng]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kthyng]

Ok it looks good to me!

[kthyng]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.00656 is OK
- 10.1016/b978-012372560-8/50002-4 is OK
- 10.1101/343079 is OK
- 10.1016/j.softx.2019.100369 is OK
- 10.4135/9781412950657.n33 is OK
- 10.1038/nbt.3820 is OK
- oi.org/10.1101/631952 is OK
- doi.org/10.3389/fninf.2014.00008 is OK
- doi.org/10.3389/fninf.2019.00064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1701

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1701, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02343 joss-papers#1702
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02343
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats to @agahkarakuzu and @mathieuboudreau on your new publication!! Thanks to editor @Kevin-Mattheus-Moerman
and reviewers @grlee77, @mfroeling, and @62442katieb. We wouldn't be able to do this without your time and expertise.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.02343/status.svg)](https://doi.org/10.21105/joss.02343)

HTML:
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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02343/status.svg
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