[REVIEW]: fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data about joss-reviews HOT 74 CLOSED

@elliohow congratulations on this paper!

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

from joss-reviews.

... can I just second comment by @mstimberg. we found the reviews very helpful and the process excellent (and @elliohow will now have sky-high expectations of what reviews should be like elsewhere 😀). 🙏

from joss-reviews.

@billbrod and @ZeitgeberH, thank you so much for your detailed reviews and your timely replies, and thank you @elliohow for taking all reviewer comments into account. I will take it from here and finalize the submission process.

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👋 @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

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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 😄

from joss-reviews.

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

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👋🏼 @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

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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.

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👋 @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!

from joss-reviews.

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

from joss-reviews.

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".

from joss-reviews.

@ZeitgeberH and @billbrod, thanks for your feedback.

@elliohow thanks for letting us know, please comment here as soon as you have a revised version of the paper. I'd appreciate if you could make the changes before the end of the week, so that we can advance with the review.

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Excellent, then I @mstimberg I also recommend this for acceptance! (Though @elliohow I think you need to retrigger the paper build one more time).

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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

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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

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Wordcount for paper.md is 714

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

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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?

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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?
  • 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?
  • 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)?
  • 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?
  • elliohow/fMRI_ROI_Analysis_Tool#38
  • 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
  • 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?
  • elliohow/fMRI_ROI_Analysis_Tool#37

from joss-reviews.

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?

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@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?

from joss-reviews.

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!

from joss-reviews.

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!

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👋 @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?

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@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.

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@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 👍 .

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👋 @elliohow just checking in, how are things going with the open issues?

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Hi @mstimberg and @elliohow
I have worked through the test and tutorial part. The package (version 1.3.6) is now fully functional in my WSL2 environment . From my side, remaining issue is the improvement on the paper (State of the field and associated references).

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Sorry this fell off my plate for a while. I agree with @ZeitgeberH about the paper, and I'll double check that everything works on my environment / if I have more feedback about that either today or Monday.

from joss-reviews.

Hi @mstimberg, apologies for the delay. Myself and the co-authors are still determining the best ways to respond to the comments about the paper and revise it in light of those comments. I hope to have a revised version for the reviewers to look over very soon.

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@editorialbot commands

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Hello @elliohow, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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@editorialbot check references

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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
- 10.1002/hbm.26081 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

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@editorialbot generate preprint

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📄 Preprint file created: Find it here in the Artifacts list 📄

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@editorialbot generate pdf

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

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⚠️ An error happened when generating the pdf.

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Hi @mstimberg, here is the revised version of the paper. I'm not quite sure where the error is occuring as the pdf seems to have generated okay.

Tagging my co-authors: @schluppeck & @ppzstf

from joss-reviews.

Thank you for the updated manuscript @elliohow , I think the error is some GitHub API hiccup that we can ignore.

@ZeitgeberH and @billbrod , please have a look at the updated paper and check whether it addresses your concerns 🙏

from joss-reviews.

@mstimberg
The updated paper addressed my concerns. From my usage, It is clear that fRAT is capable of calculating ROI based metric and statistical measures with the flexibility of choosing among more than a dozen of ready-to-use atlas. I recommend acceptance.

from joss-reviews.

This paper is much clearer! My final concern is that it's not clear to me from the paper (or statement of need in the docs) that the ROIs fRAT uses are derived from anatomical atlases that the package provides (so I disagree with @ZeitgeberH that this is clear right now) -- I realize that from the conversations we've had during the review process, and it's implicit in the paper. I think it just needs an extra sentence, e.g., in the third paragraph of the paper:

The user provides a 4D fMRI timeseries as an input, from which the voxelwise maps of data quality metrics (e.g. tSNR) are computed within fRAT. Alternatively, pre-computed data quality maps can be used. In addition, the ROI analysis requires a structural scan (MPRAGE) which should be skull stripped (using FSL’s BET (Smith, 2002), or preferably, using optiBET (Lutkenhoff et al., 2014)) in order to run (Figure 3).

Then add: "fRAT matches [or analyzes or something] the structural scan with the user's choice of one of more than a dozen ready-to-use anatomical atlases to define ROIs. These ROIs are used ..." and then continue that paragraph. Currently, I don't think it's clear how ROIs are defined, and the use of the anatomical atlases is important.

Once that change is made (in both paper and docs), I recommend acceptance.

from joss-reviews.

@billbrod

Instead of changing the 3rd paragraph, what about changing the 2nd paragraph from:

fRAT relies heavily on the python library Nipype to access the analysis tools provided by FSL [@jenkinsonFSL2012].

To:

fRAT relies heavily on the analysis tools and ROI atlases provided by FSL [@jenkinsonFSL2012].

from joss-reviews.

That's good, but I still believe the paper should forefront that the ROI definitions are based on anatomical atlases (because there are many ways that ROIs can be defined, and basing them on anatomical atlases is an important analytical choice). You do say "Defining ROIs based on atlases, as is performed with fRAT, prevents a circular analysis and leading to more accurate effect size estimation", but that's the very last sentence and the only place where it's made explicit how you define them. You could change the opening of the second paragraph to "fRAT is an open source, python-based application which focuses on ROI-wise analysis of fMRI data, by providing an easy to use and flexible pipeline for converting voxelwise data into ROI-wise data based on FSL's provided anatomical atlases." To me, the difference between this sentence (or my other suggestion) and what you suggested is: you don't just rely heavily on these atlases (which sounds like they're a little incidental), their use is an analytical choice that you've made (with good reason!).

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Thank you for the suggestion @billbrod, ive made the changes to the paper and documentation now.

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@editorialbot generate pdf

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

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• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

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Version number: 1.4.0
DOI: 10.5281/zenodo.7877605

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Version number: 1.4.0 DOI: 10.5281/zenodo.7877605

Looks good to me!

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@editorialbot generate pdf

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@editorialbot check references

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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

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

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@editorialbot set 10.5281/zenodo.7877605 as archive

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Done! archive is now 10.5281/zenodo.7877605

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@editorialbot set 1.4.0 as version

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Done! version is now 1.4.0

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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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

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@editorialbot accept

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

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@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.

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@editorialbot accept

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

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@editorialbot accept

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

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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:

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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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

from joss-reviews.