[REVIEW]: Radial Interstices Enable Speedy Low-volume Imaging

[whedon]

Submitting author: @spinicist (Tobias Wood)
Repository: https://github.com/spinicist/riesling
Version: v0.6
Editor: @emdupre
Reviewer: @uecker , @MartinK84
Archive: 10.5281/zenodo.5552973

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Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

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Markdown: [![status](https://joss.theoj.org/papers/09eb68046190ebfb292ab67a52a37ce1/status.svg)](https://joss.theoj.org/papers/09eb68046190ebfb292ab67a52a37ce1)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@uecker & @MartinK84, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @uecker

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 (@spinicist) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @MartinK84

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 (@spinicist) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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. @uecker , @MartinK84 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (1491.3 files/s, 92173.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             62            529            122           4457
C/C++ Header                    43            226             81           1231
YAML                             2             18              1            170
CMake                            1              9              6            139
Markdown                         4             42              0            123
reStructuredText                 6             80             33            116
TeX                              1              9              0            101
MATLAB                           3             26             60             60
JSON                             1              0              0             20
Python                           1             15             30             10
Bourne Shell                     1              2              4              6
-------------------------------------------------------------------------------
SUM:                           125            956            337           6433
-------------------------------------------------------------------------------


Statistical information for the repository 'ac6013792f30e7c233e3b449' was
gathered on 2021/07/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Emil                             1             7              7            0.06
Emil Ljungberg                  14           612             84            3.16
Tobias Wood                    105         13737           7564           96.77

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Emil Ljungberg              232           37.9          2.9                4.31
Tobias Wood                6469           47.1          2.2                3.48

[whedon]

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

OK DOIs

- 10.1002/nbm.4493 is OK
- 10.1002/mrm.23041 is OK
- 10.1002/mrm.1241 is OK
- 10.1002/mrm.22595 is OK

MISSING DOIs

- 10.1016/j.pnmrs.2021.03.002 may be a valid DOI for title: Silent Zero TE MR Neuroimaging: Current State-of-the-Art and Future Directions

INVALID DOIs

- None

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[whedon]

👋 @MartinK84, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @uecker , please update us on how your review is going (this is an automated reminder).

[emdupre]

Hi @uecker @MartinK84 !

I know we're expecting a slightly longer review period, here, so just to flag that this is still moving forward as expected. But please do let me know if you are having any difficulties in your review process !

[MartinK84]

@emdupre I have completed my review

In my opinion, the submission meets all requirements for publication in JOSS and I highly recommend acceptance. I can confirm that all claims made by the authors are reasonable and valid. Without much work, I was able to use and apply RIESLING to my own data with very good results. There were some minor issues regarding the installation, documentation, and usage which I have resolved together with the corresponding author @spinicist over in their repository.

[emdupre]

Thank you for your review, @MartinK84 !

I am cross-linking that these discussions have taken place in spinicist/riesling#21, spinicist/riesling#22, spinicist/riesling#23, spinicist/riesling#24, spinicist/riesling#25, and spinicist/riesling#26. If I have missed any additional references, please don't hesitate to add them here.

[emdupre]

👋 Hi @uecker -- have you had a chance to take a look at the paper, and start working through the review checklist ? If you post issues on the software repo, please add a pointer to this issue so they are cross-linked.

[uecker]

Two issues I raised so far:
spinicist/riesling#27
spinicist/riesling#28

[uecker]

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 (@spinicist) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

[emdupre]

Cross-linking that spinicist/riesling#29 and spinicist/riesling#30 have also been raised in this review process !

@uecker, I noticed that the authors have responded directly in the linked issues. Could you confirm whether these responses address your concerns, or if there are any other issues that should be raised from your review of the above checklist ?

[uecker]

I also just filed an issue for the example repository:
spinicist/riesling-examples#1

[spinicist]

I have addressed the problem in the example repository by updating the example into a Notebook, which now runs successfully in MyBinder (https://hub.gke2.mybinder.org/user/spinicist-riesling-examples-xaoj7os3/lab/tree/rrsg-cgsense.ipynb).

[uecker]

My review is complete. All issues were resolved and I can highly recommend acceptance.

[emdupre]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[emdupre]

@whedon check references

[whedon]

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

OK DOIs

- 10.1002/nbm.4493 is OK
- 10.1002/mrm.23041 is OK
- 10.1002/mrm.1241 is OK
- 10.1002/mrm.22595 is OK

MISSING DOIs

- 10.1016/j.pnmrs.2021.03.002 may be a valid DOI for title: Silent Zero TE MR Neuroimaging: Current State-of-the-Art and Future Directions

INVALID DOIs

- None

[emdupre]

Thank you, @uecker and @MartinK84 for your thorough reviews and @spinicist for your impressive work on RIESLING !

At this point could you please:

• Add in the missing DOI flagged by Whedon for the Ljungberg et al (2021) reference
• Confirm formatting on the Statement of Need; i.e., whether the "major issues" identified in the first paragraph should be inline or formatted as a list
• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission 🚀

[spinicist]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[spinicist]

Thanks everyone!

@emdupre I think I have fulfilled your checklist. The tagged release is v0.6, and I have enabled Zenodo indexing of the Github repo so https://zenodo.org/badge/latestdoi/317237623 points to that release. The DOI is 10.5281/zenodo.5552973. I fixed the MD formatting (missing newlines) and added the flagged DOI.

[emdupre]

Thank you, @spinicist !

To quickly confirm : the Zenodo metadata lists the authors as Tobias Wood; Emil Ljungberg; Martin Krämer while the repository README (and paper) lists the authors as Tobias C Wood, Emil Ljungberg, Florian Wiesinger.

Can we ensure that Florian Wiesinger is included as an author in the Zenodo archive, given his authorship on the paper ? Separately, can you confirm that you intended to list Martin Krämer as an author on the Zenodo archive ?

[spinicist]

Zenodo automatically took the authors from the Github commits, including those that Martin made as part of his review. I have edited the meta-data, it should now show Florian as an author.

[emdupre]

@whedon set v0.6 as version

[whedon]

OK. v0.6 is the version.

[emdupre]

@whedon set 10.5281/zenodo.5552973 as archive

[whedon]

OK. 10.5281/zenodo.5552973 is the archive.

[emdupre]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.pnmrs.2021.03.002 is OK
- 10.1002/nbm.4493 is OK
- 10.1002/mrm.23041 is OK
- 10.1002/mrm.1241 is OK
- 10.1002/mrm.22595 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2649

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2649, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@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.03500 joss-papers#2650
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03500
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...

[kyleniemeyer]

Congratulations @spinicist on your article's publication in JOSS!

Many thanks to @uecker and @MartinK84 for reviewing this submission, and @emdupre for editing.

[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:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03500/status.svg)](https://doi.org/10.21105/joss.03500)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03500">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03500/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03500/status.svg
   :target: https://doi.org/10.21105/joss.03500

This is how it will look in your documentation:

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[spinicist]

Thanks again to everyone!