[REVIEW]: PET2BIDS: a library for converting Positron Emission Tomography data to BIDS

[editorialbot]

Submitting author: @CPernet (Cyril Pernet)
Repository: https://github.com/openneuropet/PET2BIDS/
Branch with paper.md (empty if default branch): JOSS_paper
Version: v1.3.20240502
Editor: @britta-wstnr
Reviewers: @nbeliy, @adswa, @pjtoussaint
Archive: 10.5281/zenodo.11099654

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f044fa1d888de6646a8e8dfd5931d0da/status.svg)](https://joss.theoj.org/papers/f044fa1d888de6646a8e8dfd5931d0da)

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

@nbeliy & @adswa & @pjtoussaint, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @britta-wstnr know.

✨ 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 ✨

Checklists

📝 Checklist for @nbeliy

📝 Checklist for @adswa

📝 Checklist for @pjtoussaint

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (511.1 files/s, 40250.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             14              0            173
Markdown                         1             13              0             91
YAML                             2              1              4             19
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SUM:                             4             28              4            283
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 789

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.1038/s41597-022-01164-1 is OK
- 10.1016/j.neuroimage.2015.05.049 is OK
- 10.3389/fninf.2011.00037 is OK
- 10.1385/ni:5:1:11 is OK
- 10.1177/0271678X20905433 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
- 10.3389/fninf.2021.770608 is OK
- 10.5281/zenodo.7795644 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[britta-wstnr]

@nbeliy @adswa @pjtoussaint 👋
FYI @CPernet

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot.

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link this issue (so that a link is created to this thread). That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread.

🎯 We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[nbeliy]

Review checklist for @nbeliy

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 https://github.com/openneuropet/PET2BIDS/?
• 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 (@CPernet) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[adswa]

Review checklist for @adswa

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 https://github.com/openneuropet/PET2BIDS/?
• 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 (@CPernet) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[pjtoussaint]

Review checklist for @pjtoussaint

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 https://github.com/openneuropet/PET2BIDS/?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@CPernet) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[britta-wstnr]

Looks like everyone has started their review, awesome!
Note: I will be out of office for winter break soon, so I might be slow to respond for a while. ❄️ ⛄

[CPernet]

@pjtoussaint we have pushed some updates based on the other reviewers comments

[britta-wstnr]

Hello everyone - just to say I am back in the office now. Looks like things are progressing, great!
Don't hesitate to ping me with any questions.

[britta-wstnr]

Hi everyone,
I can see the reviewers are making great progress through your checklist but some points are still open. I see @CPernet reports to have addressed some of raised points above, but others still seem to be open, e.g. here openneuropet/PET2BIDS#236
Would you mind briefly reporting where we are at, @CPernet ?
Thanks! 🙏

[CPernet]

getting there, retesting the read the doc (that crashes) and our CI -- @bendhouseart has been tasked to do those

[bendhouseart]

Yes, as Cyril mentioned I've been chipping away at the issues raised by @adswa and am currently wrapping up some changes holding @CPernet up with respect to openneuropet/PET2BIDS#236. I think that now we're all waiting on my completing and merging openneuropet/PET2BIDS PR #262.

[britta-wstnr]

@CPernet and @bendhouseart - great! Thanks a lot for the update!

[nbeliy]

Just for info, I'll be away for the next 2 week

[CPernet]

@nbeliy response posted in openneuropet/PET2BIDS#236 with the text updated - thx

[CPernet]

@adswa all the issues fixed by @bendhouseart should be all good now

[CPernet]

@britta-wstnr we had no feedback from @pjtoussaint ??

[CPernet]

thx @britta-wstnr indeed, now using the GitHub repo URL instead openneuropet/PET2BIDS@3d431db

[CPernet]

@editorialbot generate pdf

[editorialbot]

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

[britta-wstnr]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.1038/s41592-024-02237-2 is OK
- 10.1016/j.neuroimage.2015.05.049 is OK
- 10.1177/0271678X20905433 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
- 10.1385/ni:5:1:11 is OK
- 10.1038/s41597-022-01164-1 is OK
- 10.3389/fninf.2021.770608 is OK
- 10.1038/s41597-024-02959-0 is OK
- 10.7554/eLife.71774 is OK
- 10.5281/zenodo.7795644 is OK

MISSING DOIs

- No DOI given, and none found for title: Requirements and implementation of a flexible kine...
- No DOI given, and none found for title: Public nEUro
- No DOI given, and none found for title: DICOM PS3.3 2020b - Information Object Definitions
- No DOI given, and none found for title: dicm2nii
- No DOI given, and none found for title: dcm2nii
- No DOI given, and none found for title: readECAT7

INVALID DOIs

- None

[britta-wstnr]

@CPernet great, thanks!
I just checked the paper again and things look good to me. Double-checked the missing DOIs again, and they indeed seem to be "legit", no DOI given.

Time to recommend acception of the paper - from here, the EiC will take over.
Thanks again for your review work, @nbeliy @adswa and @pjtoussaint ! We value and appreciate your work ❤️

@CPernet and @bendhouseart et al., if you are not signed up yet, please consider to sign up as a reviewer for JOSS: https://reviewers.joss.theoj.org/join . You can of course also recommend this to your co-authors 😉

Thanks everyone for working on this!

[britta-wstnr]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.1038/s41592-024-02237-2 is OK
- 10.1016/j.neuroimage.2015.05.049 is OK
- 10.1177/0271678X20905433 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
- 10.1385/ni:5:1:11 is OK
- 10.1038/s41597-022-01164-1 is OK
- 10.3389/fninf.2021.770608 is OK
- 10.1038/s41597-024-02959-0 is OK
- 10.7554/eLife.71774 is OK
- 10.5281/zenodo.7795644 is OK

MISSING DOIs

- No DOI given, and none found for title: Requirements and implementation of a flexible kine...
- No DOI given, and none found for title: Public nEUro
- No DOI given, and none found for title: DICOM PS3.3 2020b - Information Object Definitions
- No DOI given, and none found for title: dicm2nii
- No DOI given, and none found for title: dcm2nii
- No DOI given, and none found for title: readECAT7

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5783, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@CPernet as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

• In your affiliations, please spell out USA as United States (or United States of America).

[Kevin-Mattheus-Moerman]

@CPernet 👋

[mnoergaard]

Hi @Kevin-Mattheus-Moerman. This should be updated now: openneuropet/PET2BIDS@fac5455

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[mnoergaard]

Looks good now - thanks, @Kevin-Mattheus-Moerman !

[mnoergaard]

We are ready to have this published :-)

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Galassi
  given-names: Anthony
  orcid: "https://orcid.org/0000-0001-6550-4574"
- family-names: Norgaard
  given-names: Martin
  orcid: "https://orcid.org/0000-0003-2131-5688"
- family-names: Thomas
  given-names: Adam G.
  orcid: "https://orcid.org/0000-0002-2850-1419"
- family-names: Gonzalez-Escamilla
  given-names: Gabriel
  orcid: "https://orcid.org/0000-0002-7209-1736"
- family-names: Svarer
  given-names: Claus
  orcid: "https://orcid.org/0000-0001-7811-1825"
- family-names: Rorden
  given-names: Chris
  orcid: "https://orcid.org/0000-0002-7554-6142"
- family-names: Matheson
  given-names: Granville J.
  orcid: "https://orcid.org/0000-0002-5646-4547"
- family-names: Knudsen
  given-names: Gitte M.
  orcid: "https://orcid.org/0000-0003-1508-6866"
- family-names: Innis
  given-names: Robert B.
  orcid: "https://orcid.org/0000-0003-1238-7209"
- family-names: Ganz
  given-names: Melanie
  orcid: "https://orcid.org/0000-0002-9120-8098"
- family-names: Eierud
  given-names: Cyrus
  orcid: "https://orcid.org/0000-0002-9942-676X"
- family-names: Bilgel
  given-names: Murat
  orcid: "https://orcid.org/0000-0001-5042-7422"
- family-names: Pernet
  given-names: Cyril
  orcid: "https://orcid.org/0000-0003-4010-4632"
doi: 10.5281/zenodo.11099654
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Galassi
    given-names: Anthony
    orcid: "https://orcid.org/0000-0001-6550-4574"
  - family-names: Norgaard
    given-names: Martin
    orcid: "https://orcid.org/0000-0003-2131-5688"
  - family-names: Thomas
    given-names: Adam G.
    orcid: "https://orcid.org/0000-0002-2850-1419"
  - family-names: Gonzalez-Escamilla
    given-names: Gabriel
    orcid: "https://orcid.org/0000-0002-7209-1736"
  - family-names: Svarer
    given-names: Claus
    orcid: "https://orcid.org/0000-0001-7811-1825"
  - family-names: Rorden
    given-names: Chris
    orcid: "https://orcid.org/0000-0002-7554-6142"
  - family-names: Matheson
    given-names: Granville J.
    orcid: "https://orcid.org/0000-0002-5646-4547"
  - family-names: Knudsen
    given-names: Gitte M.
    orcid: "https://orcid.org/0000-0003-1508-6866"
  - family-names: Innis
    given-names: Robert B.
    orcid: "https://orcid.org/0000-0003-1238-7209"
  - family-names: Ganz
    given-names: Melanie
    orcid: "https://orcid.org/0000-0002-9120-8098"
  - family-names: Eierud
    given-names: Cyrus
    orcid: "https://orcid.org/0000-0002-9942-676X"
  - family-names: Bilgel
    given-names: Murat
    orcid: "https://orcid.org/0000-0001-5042-7422"
  - family-names: Pernet
    given-names: Cyril
    orcid: "https://orcid.org/0000-0003-4010-4632"
  date-published: 2024-08-23
  doi: 10.21105/joss.06067
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6067
  title: "PET2BIDS: a library for converting Positron Emission
    Tomography data to BIDS"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06067"
  volume: 9
title: "PET2BIDS: a library for converting Positron Emission Tomography
  data to BIDS"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06067 joss-papers#5805
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06067
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...

[mnoergaard]

Many thanks @Kevin-Mattheus-Moerman and @britta-wstnr - it all looks good. @CPernet

[CPernet]

🎉🌈🦄💃👻🤘
@editorialbot close

[CPernet]

thx for taking over @mnoergaard while I'm on holiday -- all good indeed (not sure how to close the issue now)

[editorialbot]

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

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