[REVIEW]: The quest for measuring myelin with MRI - An interactive meta-analysis

[roboneuro]

Submitting author: @agahkarakuzu (Agah Karakuzu)
Repository: https://github.com/Notebook-Factory/myelin-meta-analysis
Editor: @emdupre
Reviewer: @ltetrel
Jupyter Book: http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/myelin-meta-analysis/68ae71f025a2f2a506c72525730f8c44f6a2705d/_build/html/
Repository archive: 10.5281/zenodo.6463433
Data archive: 10.5281/zenodo.6463435
Book archive: 10.5281/zenodo.6463431
Docker archive: 10.5281/zenodo.6463437

Status

Status badge code:

HTML: <a href="http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01"><img src="http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01/status.svg"></a>
Markdown: [![status](http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01/status.svg)](http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01)

Testers 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.)

Tester instructions & questions

@ltetrel, 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
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The tester guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emdupre know.

Review checklist for @ltetrel

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 NeuroLibre code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url? #8
• 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?
• 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? #5
• 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?

[roboneuro]

Hello human, I'm @roboneuro, a robot that can help you with some common managerial tasks. @ltetrel it looks like you're currently assigned to test this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/neurolibre/neurolibre-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/neurolibre/neurolibre-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@roboneuro commands

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

@roboneuro generate pdf

[roboneuro]

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

[roboneuro]

👉📄 View built NeuroLibre Notebook 📄👈

[agahkarakuzu]

@roboneuro build nl-notebook

[roboneuro]

I'm sorry dear human, I don't understand that. You can see what commands I support by typing:

@roboneuro commands

[agahkarakuzu]

@roboneuro generate nl-notebook

[roboneuro]

🌱 We are currently building your NeuroLibre notebook! Good things take time 🌱

[roboneuro]

👉📄 View built NeuroLibre Notebook 📄👈

[agahkarakuzu]

@ltetrel I have responded to the issues you raised.

Quick note, despite that my config requests binder_url as follows:

https://github.com/Notebook-Factory/myelin-meta-analysis/blob/f5ace45de1519ac42a1bbc3fd504d566f4cc8b79/content/_config.yml#L29

The BinderHub link ends up taking me to mybinder.

[ltetrel]

Ok, I replied to you in the issue.

[agahkarakuzu]

@roboneuro generate nl-notebook

[roboneuro]

I'm sorry dear human, I don't understand that. You can see what commands I support by typing:

@roboneuro commands

[agahkarakuzu]

@roboneuro generate nl-notebook

[roboneuro]

🌱 We are currently building your NeuroLibre notebook! Good things take time 🌱

[roboneuro]

👉📄 View built NeuroLibre Notebook 📄👈

[agahkarakuzu]

OK beautiful, it incorporates the latest change I made to the text, yet the BinderHub links are still pointing to mybinder.org despite _config directive is binder.conp.cloud.

[ltetrel]

Alright @agahkarakuzu , at this stage I was able to reproduce everything without any issues.
The are still (quite minor) issues, but all of them should be resolved mostly by the binder link issue: Notebook-Factory/myelin-meta-analysis#5

We are close to our first NeuroLibre completed submission!!!

[agahkarakuzu]

@roboneuro generate nl-notebook

[roboneuro]

🌱 We are currently building your NeuroLibre notebook! Good things take time 🌱

[roboneuro]

👉📄 View built NeuroLibre Notebook 📄👈

[agahkarakuzu]

@roboneuro generate nl-notebook

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2018.04.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[agahkarakuzu]

Changing neurolibre/preprints from main to master.

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2018.04.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

👋 @neurolibre/editors, this paper is ready to be accepted and published.

Check final proof 👉 neurolibre/preprints#1

If the paper PDF and Crossref deposit XML look good in neurolibre/preprints#1, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@roboneuro accept deposit=true

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2018.04.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

👋 @neurolibre/editors, this paper is ready to be accepted and published.

Check final proof 👉 neurolibre/preprints#2

If the paper PDF and Crossref deposit XML look good in neurolibre/preprints#2, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@roboneuro accept deposit=true

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2018.04.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

👋 @neurolibre/editors, this paper is ready to be accepted and published.

Check final proof 👉 neurolibre/preprints#3

If the paper PDF and Crossref deposit XML look good in neurolibre/preprints#3, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@roboneuro accept deposit=true

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2018.04.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2018.04.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

👋 @neurolibre/editors, this paper is ready to be accepted and published.

Check final proof 👉 neurolibre/preprints#4

If the paper PDF and Crossref deposit XML look good in neurolibre/preprints#4, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@roboneuro accept deposit=true

[agahkarakuzu]

@roboneuro accept deposit=true

[roboneuro]

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

[roboneuro]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.55458.neurolibre.00004 preprints#5
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.55458/neurolibre.00004
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...

[agahkarakuzu]

@roboneuro generate pdf

[agahkarakuzu]

https://neurolibre.herokuapp.com/papers/10.55458/neurolibre.00004

[roboneuro]

🎉🎉🎉 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://neurolibre.org/papers/10.55458/neurolibre.00004/status.svg)](https://doi.org/10.55458/neurolibre.00004)

HTML:
<a style="border-width:0" href="https://doi.org/10.55458/neurolibre.00004">
  <img src="https://neurolibre.org/papers/10.55458/neurolibre.00004/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://neurolibre.org/papers/10.55458/neurolibre.00004/status.svg
   :target: https://doi.org/10.55458/neurolibre.00004

This is how it will look in your documentation: