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

[editorialbot]

Submitting author: !--author-handle-->@alixlam<!--end-author-handle-- (Alix Marie Eleonore Lamouroux) Repository: https://github.com/alixlam/fmristroke Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@sappelhoff<!--end-editor-- Reviewers: @SRSteinkamp, @behinger, @mnarayan Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @alixlam. Currently, there isn't a JOSS editor assigned to your paper.

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[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 (853.1 files/s, 226901.8 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
reStructuredText                 8            153            106            287
YAML                             4             16             23            285
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
-------------------------------------------------------------------------------
SUM:                           105           1951           2244          23733
-------------------------------------------------------------------------------

Commit count by author:

    51  Alix Lamouroux
    36  Alix LAMOUROUX
    31  alixlam

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 687

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@alixlam thanks for this submission. As AEiC in am here to help with initial steps. First I need to understand if this work is in scope (topic/functionality etc it may be), and if it is mature enough in terms of our standards. On the latter I have some worries. First of all, our system has not detected an OSI approved license. Please add a plain LICENSE file to your main repository folder. Secondly I have not discovered automated testing for this project. Can you elaborate on testing, have you implemented any testing for your project?

[Kevin-Mattheus-Moerman]

@alixlam can you respond to this query :point_up:, thanks

[alixlam]

@Kevin-Mattheus-Moerman thank you for your feedback on the initial steps. I am sorry for the delay in my response. Concerning the license file, I was hoping to have some guidance on that, as they are many licenses possible on the link you provided I am not sure which one to use. On testing, I have implemented some tests for this project, and made sure that the tests are run at each push to the main branch, however maybe there are not enough ? I added today to the repository the information on the test coverage (thanks to a badge on the README), today the coverage is 71%.

[Kevin-Mattheus-Moerman]

@alixlam Unfortunately we cannot offer advice on a license to choose. So even what I share here is by no means legal advice on a license, I'll just recommend, not as an editor representing JOSS, but as a fellow researcher, some steps to understand these licenses. I would take some time at this point to understand the main types and the consequences/outcomes associated with each license. I know the OSI approved license list is very long, however if you do not have a strong license preference at the moment it is probably best to stick to a widely used license. Of those there are two main types, permissive ones (e.g. MIT, Apache 2.0) and "copy left" ones (e.g. GPL-v3). It is important to understand the difference between the two, and to first decide on that. The biggest impact here is for folks using your work, e.g. the copy left license placing constraints on people using your work in terms of the license they may use. Some see this as a beneficial property of copy-left, as it may ensure that derivatives stay free/open (under the same type of license), while others feel this is negative and that there should be more flexibility (even to make a derivative closed-source/proprietary), which leads them to permissive licenses. I recommend you read some resources on license types (e.g. https://choosealicense.com/, https://en.wikipedia.org/wiki/Open-source_license, and look for some others yourself) and to start from there.

Once again, this text here is by no means any form of legal advice on licenses, I am afraid the sole responsibility in choosing a license rests with you. Myself and JOSS have no preference in terms of the type of OSI approved license you choose.

Hope this helps.

[alixlam]

@Kevin-Mattheus-Moerman , thanks a lot for the clarification it definitely helped , I added the LICENSE file to the project.

[Kevin-Mattheus-Moerman]

@editorialbot invite @sappelhoff as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@alixlam thanks for adding that license. I have just started looking for an editor to handle this submission. One point that will come up during review is contributing guidelines, which I believe you currently do not have. I recommend you add a CONTRIBUTING.md file to your main folder, and to link to it from the README (here are some examples: https://contributing.md/example/).
Secondly please add the city and country for both affiliations on the paper, thanks.

[sappelhoff]

@editorialbot assign me as editor

[editorialbot]

Assigned! @sappelhoff is now the editor

[sappelhoff]

Hi @alixlam I will be editing your submission.

Do you have a list of potential reviewers for your project, that I could screen and use for invitations?

Please also remember to respond to this earlier request:

Secondly please add the city and country for both affiliations on the paper, thanks.

Finally, why are there a number of authors on the paper that (seemingly) have not committed to the repository?

[alixlam]

Hello, @sappelhoff thank you for your time. I do not have a list of potential reviewers unfortunately.

I will add this information right away. The other authors have indeed not comitted to the repository but have guided me in the process, I am a phd student and they are my thesis supervisors.

[sappelhoff]

I do not have a list of potential reviewers unfortunately.

Ok, no problem -- I will start trying to find some. In case you think of a suitable reviewer in the meantime, please let me know. It'd be a great help and speed up the review process.

I will add this information right away.

Great, thank you.

The other authors have indeed not committed to the repository but have guided me in the process, I am a phd student and they are my thesis supervisors.

Thanks for the explanation. For your reference, here are our guidelines as to the "responsibilities" and "criteria" of being an author for a JOSS paper: https://joss.readthedocs.io/en/latest/submitting.html#authorship

Some further points are listed under "ethics" here: https://joss.theoj.org/about#ethics

In case you haven't checked this documentation before, please check it now. If afterwards you decide that the list of authors is fine as it is, then that's fine with me!

[sappelhoff]

👋 @peterakirk @behinger @SRSteinkamp, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I will also try to send you a more formal invitation via email.

[sappelhoff]

@editorialbot add @SRSteinkamp as reviewer

[editorialbot]

@SRSteinkamp added to the reviewers list!

[sappelhoff]

👋 @a3sha2 @szorowi1 @mnarayan, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I will also try to send you a more formal invitation via email.

[mnarayan]

I won't be able to for 2 weeks.

On Mon, Apr 15, 2024, 7:41 AM Stefan Appelhoff @.***> wrote:

👋 @a3sha2 https://github.com/a3sha2 @szorowi1 https://github.com/szorowi1 @mnarayan https://github.com/mnarayan, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I will also try to send you a more formal invitation via email.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6493#issuecomment-2057028021, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFC75Z3DNXR22CS33YYA2LY5PRIZAVCNFSM6AAAAABEYDLR52VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJXGAZDQMBSGE . You are receiving this because you were mentioned.Message ID: @.***>

[behinger]

Thanks for waiting for my response, I was travelling. I can review it. As a disclaimer: my (f)MRI days are over for some years but I will manage :)

edit: I can start earliest next week

[szorowi1]

Hi all, I can review but won't be able to start for at least two more weeks. Apologies for the inconvenience!

[sappelhoff]

Thanks for waiting for my response, I was travelling. I can review it. As a disclaimer: my (f)MRI days are over for some years but I will manage :)

Thanks @behinger, I am planning to assign a team of 3 reviewers, so between all of you, all things will probably be covered!

[sappelhoff]

@editorialbot add @behinger as reviewer

[editorialbot]

@behinger added to the reviewers list!

[sappelhoff]

Thanks also @szorowi1 and @mnarayan for volunteering. It is totally fine to only be able to start the review in 2 or 3 weeks from now.

For now I will assign @mnarayan as a reviewer. Would you be willing to serve as a potential backup @szorowi1?

[sappelhoff]

@editorialbot add @mnarayan as reviewer

[editorialbot]

@mnarayan added to the reviewers list!

[sappelhoff]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6636.

[szorowi1]

@sappelhoff, absolutely I'm happy to serve as a backup. Thank you!