[REVIEW]: fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data #5200

editorialbot · 2023-03-01T08:53:05Z

Submitting author: @elliohow (Elliot Howley)
Repository: https://github.com/elliohow/fMRI_ROI_Analysis_Tool
Branch with paper.md (empty if default branch):
Version: 1.4.0
Editor: @mstimberg
Reviewers: @ZeitgeberH, @billbrod
Archive: 10.5281/zenodo.7877605

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/cc9c0cb3b12abaf30c8381728d3229d7/status.svg)](https://joss.theoj.org/papers/cc9c0cb3b12abaf30c8381728d3229d7)

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

@ZeitgeberH & @billbrod, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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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 ✨

Checklists

📝 Checklist for @ZeitgeberH

📝 Checklist for @billbrod

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-03-01T08:53:07Z

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

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editorialbot · 2023-03-01T08:54:30Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.17 s (33.3 files/s, 19005.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSS                              1           1243             13           9224
Python                          16           1816            343           5188
SVG                              1              0              0           3150
TOML                             7             68             64            431
reStructuredText                 9            118            115            273
TeX                              1              6              0            118
Markdown                         2             25              0             69
YAML                             1              4              7             10
JavaScript                       1              0              1              2
-------------------------------------------------------------------------------
SUM:                            39           3280            543          18465
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-03-01T08:54:31Z

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

OK DOIs

- 10.1002/mrm.1124 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1371/journal.pone.0115551 is OK
- 10.1016/j.neuroimage.2006.09.032 is OK
- 10.1002/(SICI)1522-2594(199911)42:5<952::AID-MRM16>3.0.CO;2-S is OK
- 10.1002/hbm.10062 is OK
- 10.1371/journal.pone.0077089 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-01T08:54:32Z

Wordcount for paper.md is 714

editorialbot · 2023-03-01T08:55:27Z

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

mstimberg · 2023-03-01T09:00:11Z

👋🏼 @elliohow @ZeitgeberH @billbrod this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please feel free to ping me (@mstimberg) if you have any questions/concerns.

ZeitgeberH · 2023-03-01T14:02:18Z

Review checklist for @ZeitgeberH

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/elliohow/fMRI_ROI_Analysis_Tool?
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 (@elliohow) 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?

billbrod · 2023-03-01T16:33:10Z

Review checklist for @billbrod

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/elliohow/fMRI_ROI_Analysis_Tool?
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 (@elliohow) 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?
- [JOSS Review] Installation elliohow/fMRI_ROI_Analysis_Tool#40
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?
- [JOSS review] Documentation statement of need elliohow/fMRI_ROI_Analysis_Tool#36
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)?
- [JOSS Review] Functionality documentation and non-GUI use elliohow/fMRI_ROI_Analysis_Tool#46
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [JOSS Review] Tests? elliohow/fMRI_ROI_Analysis_Tool#38
- [JOSS Review] Automated tests? elliohow/fMRI_ROI_Analysis_Tool#45
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
- [JOSS Review] Community guidelines elliohow/fMRI_ROI_Analysis_Tool#39

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?
- [JOSS Review] Any citations using this method or demonstrating its need? elliohow/fMRI_ROI_Analysis_Tool#37

mstimberg · 2023-03-13T13:30:43Z

👋 @billbrod no hurry performing the actual review, of course, but could I ask you to check the first two boxes (conflict of interest/code of conduct) of the checklist fairly soon (or let me know if you have any issue, obviously!)? Thanks!

elliohow · 2023-03-16T17:13:09Z

Issue regarding running fRAT on WSL2:
elliohow/fMRI_ROI_Analysis_Tool#35

ZeitgeberH · 2023-03-16T20:21:07Z

Hi @elliohow
Could you add a section in your software paper to satisfy this requirement "State of the field: Do the authors describe how this software compares to other commonly-used packages?".
For example, I think you could elaborate the last point towards the end of your abstract "There is currently a lack of easy-to-use tools to analyse these metrics simultaneously across multiple ROI".

billbrod · 2023-03-22T16:21:36Z

Hi @elliohow Could you add a section in your software paper to satisfy this requirement "State of the field: Do the authors describe how this software compares to other commonly-used packages?". For example, I think you could elaborate the last point towards the end of your abstract "There is currently a lack of easy-to-use tools to analyse these metrics simultaneously across multiple ROI".

Yes, I want to second this. In particular -- to what extent is fRAT an infrastructure / facilitation tool (like Nipype or fMRIPrep), making it easier to correctly run analyses that can be already be done using existing tools, and to what extent is it implementing novel (analysis, visualization, statistical) methods?

billbrod · 2023-03-22T16:23:17Z

@mstimberg , this is more of a question about JOSS (since this is my first review) -- does JOSS allow / encourage explicit descriptions of author contributions? @elliohow has written (essentially) all the code and, following standard procedure in neuroscience/psychology, I'm thus assuming the other two authors are supervisors / involved in the conception of the package, but that's not made explicit anywhere. Should it be?

mstimberg · 2023-03-23T10:26:45Z

Hi @billbrod. JOSS does not currently require/encourage contribution statements as part of the paper, but the authors are welcome to clarify contributions here on the reviewing thread. The basic JOSS policy is that the authors themselves assume responsibility for who should be credited, and that all co-authors agree to be accountable for all aspects of the work. Code contributions are just one possible type of contribution and definitely not mandatory to be a co-author. On the other hand, we do ask for some active involvement in the project (i.e. just being the head of a research group isn't enough). Hope that makes things clearer!

billbrod · 2023-03-23T15:22:30Z

Hi @billbrod. JOSS does not currently require/encourage contribution statements as part of the paper, but the authors are welcome to clarify contributions here on the reviewing thread. The basic JOSS policy is that the authors themselves assume responsibility for who should be credited, and that all co-authors agree to be accountable for all aspects of the work. Code contributions are just one possible type of contribution and definitely not mandatory to be a co-author. On the other hand, we do ask for some active involvement in the project (i.e. just being the head of a research group isn't enough). Hope that makes things clearer!

Yes, thank you!

mstimberg · 2023-03-30T09:56:17Z

👋 @elliohow I saw that you've already discussed and fixed some of the issues raised by the reviewers 😊
Could you give me a rough estimate of when you will be able to address the remaining issues?

elliohow · 2023-03-30T15:37:01Z

@mstimberg Have had a bit of friction getting fRAT set up with Linux and WSL2 due to some unexpected bugs, but hopefully all fixed now (🤞). I hope to have the remaining issues addressed by the end of next week.

mstimberg · 2023-03-30T16:16:26Z

@mstimberg Have had a bit of friction getting fRAT set up with Linux and WSL2 due to some unexpected bugs, but hopefully all fixed now (crossed_fingers). I hope to have the remaining issues addressed by the end of next week.

Great, thanks for the feedback 👍 .

mstimberg · 2023-05-04T12:47:04Z

@editorialbot check references

editorialbot · 2023-05-04T12:47:17Z

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

OK DOIs

- 10.1002/mrm.1124 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1371/journal.pone.0184661 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.1101/295048 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1038/jcbfm.2010.86 is OK
- 10.1371/journal.pone.0115551 is OK
- 10.1177/2515245920928009 is OK
- 10.1016/j.neuroimage.2006.09.032 is OK
- 10.1016/j.neuroimage.2021.117965 is OK
- 10.1016/j.neuroimage.2004.12.002 is OK
- 10.1002/hbm.10062 is OK
- 10.1371/journal.pone.0077089 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-04T12:48:35Z

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

mstimberg · 2023-05-04T12:52:07Z

@editorialbot set 10.5281/zenodo.7877605 as archive

editorialbot · 2023-05-04T12:52:09Z

Done! archive is now 10.5281/zenodo.7877605

mstimberg · 2023-05-04T12:52:40Z

@editorialbot set 1.4.0 as version

editorialbot · 2023-05-04T12:52:42Z

Done! version is now 1.4.0

mstimberg · 2023-05-04T12:53:12Z

@editorialbot recommend-accept

editorialbot · 2023-05-04T12:53:13Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-04T12:53:24Z

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

OK DOIs

- 10.1002/mrm.1124 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1371/journal.pone.0184661 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.1101/295048 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1038/jcbfm.2010.86 is OK
- 10.1371/journal.pone.0115551 is OK
- 10.1177/2515245920928009 is OK
- 10.1016/j.neuroimage.2006.09.032 is OK
- 10.1016/j.neuroimage.2021.117965 is OK
- 10.1016/j.neuroimage.2004.12.002 is OK
- 10.1002/hbm.10062 is OK
- 10.1371/journal.pone.0077089 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-04T12:55:24Z

👋 @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#4197, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

schluppeck · 2023-05-08T18:57:42Z

@editorialbot accept

editorialbot · 2023-05-08T18:57:43Z

I'm sorry @schluppeck, I'm afraid I can't do that. That's something only eics are allowed to do.

Kevin-Mattheus-Moerman · 2023-05-10T16:07:09Z

@elliohow @mstimberg I've reviewed the archive, the repository, and the paper and all seems in order. I will now proceed to accept this work in JOSS.

Kevin-Mattheus-Moerman · 2023-05-10T16:07:18Z

@editorialbot accept

editorialbot · 2023-05-10T16:07:19Z

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

Kevin-Mattheus-Moerman · 2023-05-11T08:28:30Z

@editorialbot accept

editorialbot · 2023-05-11T08:28:31Z

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

editorialbot · 2023-05-11T08:31:05Z

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: Howley
  given-names: Elliot
  orcid: "https://orcid.org/0000-0002-3868-2516"
- family-names: Francis
  given-names: Susan
  orcid: "https://orcid.org/0000-0003-0903-7507"
- family-names: Schluppeck
  given-names: Denis
  orcid: "https://orcid.org/0000-0002-0634-7713"
contact:
- family-names: Howley
  given-names: Elliot
  orcid: "https://orcid.org/0000-0002-3868-2516"
doi: 10.5281/zenodo.7877605
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Howley
    given-names: Elliot
    orcid: "https://orcid.org/0000-0002-3868-2516"
  - family-names: Francis
    given-names: Susan
    orcid: "https://orcid.org/0000-0003-0903-7507"
  - family-names: Schluppeck
    given-names: Denis
    orcid: "https://orcid.org/0000-0002-0634-7713"
  date-published: 2023-05-11
  doi: 10.21105/joss.05200
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5200
  title: "fRAT: an interactive, Python-based tool for region-of-interest
    summaries of functional imaging data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05200"
  volume: 8
title: "fRAT: an interactive, Python-based tool for region-of-interest
  summaries of functional imaging data"

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.

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editorialbot · 2023-05-11T08:31:12Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-05-11T08:31:13Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-05-11T08:31:14Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05200 joss-papers#4220
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05200
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

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Kevin-Mattheus-Moerman · 2023-05-11T08:58:45Z

@elliohow congratulations on this paper!

@mstimberg thanks for editing, and a special thanks to the reviewers: @ZeitgeberH, @billbrod

editorialbot · 2023-05-11T08:58:47Z

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

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elliohow · 2023-05-11T14:54:07Z

Thank you @billbrod, @ZeitgeberH & @mstimberg for being so thorough in your reviews, the software and paper has benefited immensely from the process, especially in terms of making fRAT multi platform 😄

billbrod · 2023-05-11T14:55:49Z

Happy to review, glad it was useful, and congrats on the acceptance!

editorialbot added JavaScript Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Mar 1, 2023

editorialbot assigned mstimberg Mar 1, 2023

editorialbot mentioned this issue Mar 1, 2023

[PRE REVIEW]: fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data #5188

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 4, 2023

editorialbot added accepted published Papers published in JOSS labels May 11, 2023

Kevin-Mattheus-Moerman closed this as completed May 11, 2023

[REVIEW]: fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data #5200

[REVIEW]: fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data #5200

Comments

editorialbot commented Mar 1, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

editorialbot commented Mar 1, 2023

mstimberg commented Mar 1, 2023

ZeitgeberH commented Mar 1, 2023 • edited

Review checklist for @ZeitgeberH

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

billbrod commented Mar 1, 2023 • edited

Review checklist for @billbrod

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mstimberg commented Mar 13, 2023

elliohow commented Mar 16, 2023 • edited

ZeitgeberH commented Mar 16, 2023

billbrod commented Mar 22, 2023

billbrod commented Mar 22, 2023

mstimberg commented Mar 23, 2023

billbrod commented Mar 23, 2023

mstimberg commented Mar 30, 2023

elliohow commented Mar 30, 2023

mstimberg commented Mar 30, 2023

mstimberg commented May 4, 2023

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mstimberg commented May 4, 2023

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schluppeck commented May 8, 2023

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Kevin-Mattheus-Moerman commented May 10, 2023

Kevin-Mattheus-Moerman commented May 10, 2023

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Kevin-Mattheus-Moerman commented May 11, 2023

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Kevin-Mattheus-Moerman commented May 11, 2023

editorialbot commented May 11, 2023

elliohow commented May 11, 2023 • edited

billbrod commented May 11, 2023

editorialbot commented Mar 1, 2023 •

edited

ZeitgeberH commented Mar 1, 2023 •

edited

billbrod commented Mar 1, 2023 •

edited

elliohow commented Mar 16, 2023 •

edited

elliohow commented May 11, 2023 •

edited