[REVIEW]: fMRIStroke: A preprocessing pipeline for fMRI Data from Stroke patients

[editorialbot]

Submitting author: @alixlam (Alix Marie Eleonore Lamouroux)
Repository: https://github.com/alixlam/fmristroke
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @sappelhoff
Reviewers: @SRSteinkamp, @behinger, @mnarayan
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2090e00675cc4caf9978351a79bd24c3"><img src="https://joss.theoj.org/papers/2090e00675cc4caf9978351a79bd24c3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2090e00675cc4caf9978351a79bd24c3/status.svg)](https://joss.theoj.org/papers/2090e00675cc4caf9978351a79bd24c3)

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

@SRSteinkamp & @behinger & @mnarayan, 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 @sappelhoff 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 @SRSteinkamp

📝 Checklist for @behinger

[editorialbot]

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

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1016/j.mri.2009.02.004 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.5281/zenodo.10403681 is OK
- 10.1177/0271678X15614846 is OK
- 10.1177/0271678X17709198 is OK
- 10.1016/j.nicl.2017.10.027 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (861.5 files/s, 225867.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              6              1            106          12326
Python                          63           1700           2002           6852
JSON                            17              5              0           3143
CSV                              1              0              0            401
YAML                             5             32             26            360
reStructuredText                 8            154            109            287
make                             2             39              6            229
TeX                              1              5              0             91
Markdown                         1             19              0             48
TOML                             1              5              0             45
DOS Batch                        1              8              1             26
INI                              1              4              0             22
-------------------------------------------------------------------------------
SUM:                           107           1972           2250          23830
-------------------------------------------------------------------------------

Commit count by author:

    51	Alix Lamouroux
    36	Alix LAMOUROUX
    34	alixlam

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 689

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

[sappelhoff]

Hello again! 👋


@behinger, @mnarayan, @SRSteinkamp

FYI @alixlam

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 (above).

✅ 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 to #6636 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 if you are unsure about something!

🎯 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.

[SRSteinkamp]

Review checklist for @SRSteinkamp

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/alixlam/fmristroke?
• 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 (@alixlam) 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?

[SRSteinkamp]

As seen above, create an issue regarding the mismatched between the listed installation requirements and python verison: alixlam/fmristroke#11
Maybe someone else has a better idea of good practices writing requirements.txts .

[behinger]

Review checklist for @behinger

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/alixlam/fmristroke?
• 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 (@alixlam) 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?

[sappelhoff]

Hi all!

@behinger, @SRSteinkamp -- I can see you have already made a lot of progress in your review! Thank you :-) What is your expected timeline for completing your part? Are there some issues that will take longer (e.g., because of iterations with @alixlam)? What's the general status?

@mnarayan I haven't heard from you in some weeks, do you still intend to volunteer as a reviewer for this project? If so, what's your expected timeline for starting this review?

[behinger]

Hi! Thanks for asking. I think we are both waiting for alixlam to post some test-data / procedure. alixlam/fmristroke#14 (comment) to get us up to speed.

[sappelhoff]

Hey @alixlam 👋 could you please supply a short update on your efforts on adding some test-data / procedure?

[alixlam]

Hello, so sorry for the time taken to respond. I did find open data to share and ran fMRIprep on it to have the necessary derivatives to test the repository. However, I am not sure it is a good idea to add the data files directly to the repository as they are quite heavy files. Do you have any suggestions on how to share them ? @sappelhoff @behinger

[behinger]

You could upload them to osf (or fig share if you prefer), and link it. Then write a short documentation page how to access+run these data. Typically open euro is cc-by, so you can easily rehost.

I would not necessarily run a system unit-test with them if they cannot be made smaller.

[sappelhoff]

Thanks for your reply @alixlam and for finding appropriate data. I agree with @behinger on how to handle them.

[sappelhoff]

Hey @alixlam 👋 do you have a status update for us? How is the uploading of the data and the writing of documentation on how to access and use it going?

[alixlam]

Some data can be found here : https://osf.io/5z4ry/. With raw data and fmriprep derivatives. The documentation has been updated especially the Usage Notes part.

[sappelhoff]

Hey @alixlam I can see some recent activity in alixlam/fmristroke#17 (comment)

Could you please report on your expected timeline to address other issues raised by the reviewers, such as:

• Minor suggested edits to the paper alixlam/fmristroke#16
• Minor issues alixlam/fmristroke#14