[REVIEW]: Open-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7T

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@Cadaei-Yuvxvs@emdupre<!--end-editor-- Reviewers: @a3sha2, @kaczmarj Archive: 10.5281/zenodo.6874987

Status

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Markdown: [![status](https://joss.theoj.org/papers/9dff6ac0bfc6c3092c8e37ee2f17bdfb/status.svg)](https://joss.theoj.org/papers/9dff6ac0bfc6c3092c8e37ee2f17bdfb)

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

@a3sha2 & @kaczmarj, 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 @emdupre 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 @kaczmarj

📝 Checklist for @a3sha2

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (217.4 files/s, 43910.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           3            251            104           1060
Markdown                         2             56              0            188
TeX                              1              9              0             88
YAML                             2              2              4             36
Bourne Shell                     1              2              0             18
-------------------------------------------------------------------------------
SUM:                             9            320            108           1390
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1294

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.media.2007.06.004 is OK
- 10.1016/j.neuroimage.2020.117287 is OK
- 10.17605/osf.io/zge9t is OK
- 10.1016/j.neurobiolaging.2019.07.019 is OK
- 10.1111/nan.12709 is OK
- 10.1136/jnnp-2017-315795 is OK
- 10.1109/tpami.2012.143 is OK
- 10.1016/j.pscychresns.2018.04.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

kaczmarj commented 2 years ago

Review checklist for @kaczmarj

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Cadaei-Yuvxvs/OSHy-X?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Cadaei-Yuvxvs) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- to me, the most significant scholarly effort in this project is the creation of the 20 atlases. the code for the segmentation tool is quite short (all of the functional components of the tool are in the file OSHy.py, which has 413 source lines of code).

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
- i do not have the expertise to comment on the quality of hypothalamic and fornix segmentations, but i have run the software successfully and visualized the output.
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- i opened https://github.com/Cadaei-Yuvxvs/OSHy-X/issues/5 regarding installing and using this package outside of a container. as written, it appears that OSHy-X is meant to run in a container, and i wanted to confirm this.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- i opened https://github.com/Cadaei-Yuvxvs/OSHy-X/issues/6 requesting descriptions of some of the output files.
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- i opened https://github.com/Cadaei-Yuvxvs/OSHy-X/issues/7 asking to add tests of the containerized tool. currently, the repository tests the python components but not on real data and not in the environment that end users would use.
[ ] 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
- I opened https://github.com/Cadaei-Yuvxvs/OSHy-X/issues/4 regarding adding a CONTRIBUTING file to the repository. Other than this, the repository's README explains how to report issues and seek support.

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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 and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- i opened https://github.com/Cadaei-Yuvxvs/OSHy-X/issues/8 requesting comparisons with freesurfer's recon-all workflow. i think recon-all is one of the more popular tools for brain MRI segmentation.
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

emdupre commented 2 years ago

Hi @a3sha2 and @kaczmarj 👋 Thanks again for agreeing to review this submission ! The review will take place in this issue. As you've already seen, you can generate your individual reviewer checklists by asking editorialbot directly with @\editorialbot generate my checklist

In working through the checklist, you're likely to have specific feedback on OSHy-X. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

a3sha2 commented 2 years ago

Review checklist for @a3sha2

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Cadaei-Yuvxvs/OSHy-X?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Cadaei-Yuvxvs) 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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 and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

a3sha2 commented 2 years ago

@emdupre pls the link of the paper is broken. https://github.com/openjournals/joss-papers/blob/joss.04313/joss.04313/10.21105.joss.04313.pdf

a3sha2 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

emdupre commented 2 years ago

@a3sha2 thanks for checking on this ! I also noticed the error in displaying the compiled PDF document over the weekend, but there's no reported error in the GH action logs and the document is now visible. So, I think it was likely transitory ! I'll monitor in case this happens again, though.

kaczmarj commented 2 years ago

@emdupre - i finished my review in https://github.com/openjournals/joss-reviews/issues/4368#issuecomment-1116524168. i made several issues in the OSHy-X repository, and i linked them all here.

emdupre commented 2 years ago

Thank you, @kaczmarj, for your review ! I noticed that the authors have begun to address your comments, and I will continue to track progress directly in the linked GitHub issues (thank you for opening those, too !).

emdupre commented 2 years ago

👋 Hi @a3sha2, and thank you for starting your review ! I wanted to check in on its current status.

Is there anything blocking you, or any information I can provide to assist in this process ?

Cadaei-Yuvxvs commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Cadaei-Yuvxvs commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Cadaei-Yuvxvs commented 2 years ago

Dear @a3sha2, do you have any specific feedback about this paper? We have addressed and completed issues opened by @kaczmarj regarding automated tests, functionality documentation, state of the field, community guidelines, and installation. We would be very keen to hear your thoughts and address them to improve our work!

emdupre commented 2 years ago

Thank you for following up on this, @Cadaei-Yuvxvs ! I've been corresponding with @a3sha2 via email, and he has confirmed that he'll be able to finalize his review in the next few days.

I understand that this delay has frustrating, but I appreciate your patience throughout this process.

a3sha2 commented 2 years ago

@Cadaei-Yuvxvs sorry for replying late. I had nothing much to add. Most of the issues I would have raised are already asked by @kaczmarj . I asked a question on issues page. I just want to know if only T1w scan will be enough if there is no T2w scan

I can run the docker image completely welldone to the team

@emdupre

kaczmarj commented 2 years ago

@emdupre - in my initial checklist review (https://github.com/openjournals/joss-reviews/issues/4368#issuecomment-1116524168), i left some boxes unchecked and made issues for each of those items. the authors have addressed these comments. should i check those boxes now? or is it sufficient to say that i am now satisfied as a reviewer?

Cadaei-Yuvxvs commented 2 years ago

Thank you @a3sha2 :) Very kglad that we've raised most of the issues you raised. I've just posted a reply to the issue you opened for OSHy-X. https://github.com/Cadaei-Yuvxvs/OSHy-X/issues/16

a3sha2 commented 2 years ago

@emdupre I am satisfied with authors response

emdupre commented 2 years ago

Thank you, @kaczmarj and @a3sha2 ! Confirming that you've both signed off that the submission meets JOSS's publication requirements in its current form.

@Cadaei-Yuvxvs, I'm going to run a few additional checks to make sure that all of the editorial requirements are also met !

emdupre commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.media.2007.06.004 is OK
- 10.1016/j.neuroimage.2020.117287 is OK
- 10.1016/S0896-6273(02)00569-X is OK
- 10.17605/osf.io/zge9t is OK
- 10.1016/j.neurobiolaging.2019.07.019 is OK
- 10.1111/nan.12709 is OK
- 10.1136/jnnp-2017-315795 is OK
- 10.1109/tpami.2012.143 is OK
- 10.1016/j.pscychresns.2018.04.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

emdupre commented 2 years ago

Thanks again for your patience here, @Cadaei-Yuvxvs ! A few small asks on the paper itself :

[ ] Could you please update the text under the Tool subsection of Methodology to fix the formatting of the Wang reference; i.e., Joint Label Fusion (JLF) [@Wang:2013] --> Joint Label Fusion (JLF; @Wang:2013)
[ ] Please add a reference for MriResearchTools, as currently only the 0.5.2 version number is listed.
[ ] On L65 in Performance, please add a comma after "however."
[ ] In the Atlas subsection of Methodology, you note that "acquisition parameters have been outlined previously" but point to Chang et al., 2022, which is currently listed as an unpublished work. Has this reference since been published, or is there a place where readers could access the acquisition parameters ?
[ ] Figure 4 caption: It's currently unclear what the "deep learning method" refers to, as your citations currently only point to the Billot (2020) reference as a deep learning method (Statement of Need) but suggest that it only applies to the hypothalamus (Performance). Could you please clarify the figure caption ?
[ ] Update the journal on the Wolff reference from "Psychiatry research. Neuroimaging" to "Psychiatry Research: Neuroimaging".

After making these edits, could you then please :

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare or an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata (e.g., the JOSS paper and software archive have the same title and author listing)
[ ] List the DOI of the archived version here.

I can then move forward with accepting the submission 🚀

Cadaei-Yuvxvs commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

Cadaei-Yuvxvs commented 2 years ago

Thanks very much @emdupre! I have made the edits requested.

In regards to the acquisition parameters - I have updated the reference to our atlas repository instead, which now has the parameters in its wiki. Our unpublished work is currently undergoing revisions with the European Journal of Neurology.

Let me know if there's anything else that needs editing 😊

I have made a tagged release: OSHy-X v0.4: https://github.com/Cadaei-Yuvxvs/OSHy-X/releases/tag/0.4 The archive is now uploaded to Zenodo and I have checked that the metadata is correct.

emdupre commented 2 years ago

@editorialbot set 0.4 as version

editorialbot commented 2 years ago

Done! version is now 0.4

emdupre commented 2 years ago

@editorialbot set 10.5281/zenodo.6874987 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6874987

emdupre commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

emdupre commented 2 years ago

@openjournals/joss-eics I think this article is ready for recommend-accept but the PDF compilation is silently failing. Any suggestions how to approach debugging this, or if the issue is more likely on the editorial infra ?

Cadaei-Yuvxvs commented 2 years ago

@emdupre Thank you for following this up! The PDF compilation appears to be working now :)

emdupre commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

emdupre commented 2 years ago

Thanks, @Cadaei-Yuvxvs ! I'm really not sure why that's happening sporadically, but if it's stable for now I'll go ahead and move forward as-is. I'll let the corresponding EiC confirm when they do their final checks on the paper that there's nothing on the infra side that I'm missing :)

emdupre commented 2 years ago

Sorry, in reviewing the final draft it looks like one small point still needs to be addressed :

Could you please update the text under the Tool subsection of Methodology to fix the formatting of the Wang reference; i.e., Joint Label Fusion (JLF) [@Wang:2013] --> Joint Label Fusion (JLF; @Wang:2013)

The same issue would also apply to the (new !) MriResearchTools (v0.5.2; [@Eckstein:2022]) reference. In both cases, you should be able to drop the square brackets entirely.

Cadaei-Yuvxvs commented 2 years ago

@emdupre Apologies for that. I've now dropped the square brackets for these two references in paper.md. The references now look like

Joint Label Fusion (JLF; Wang et al. (2013))

Cadaei-Yuvxvs commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

emdupre commented 2 years ago

Thank you, @Cadaei-Yuvxvs !

I'm now happy to recommend OSHy-X to the EIC team for publication -- congratulations on this impressive effort !

emdupre commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

openjournals / joss-reviews