[REVIEW]: GIRFReco.jl: An open-source pipeline for spiral MRI reconstruction in Julia #5877

editorialbot · 2023-09-26T07:30:56Z

Submitting author: @alexjaffray (Alexander Jaffray)
Repository: https://github.com/BRAIN-TO/GIRFReco.jl
Branch with paper.md (empty if default branch):
Version: v0.1.7
Editor: @Kevin-Mattheus-Moerman
Reviewers: @cncastillo, @mathieuboudreau, @felixhorger
Archive: 10.5281/zenodo.11075548

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1b05a7a790f6fbc4bb503524f71ceb45/status.svg)](https://joss.theoj.org/papers/1b05a7a790f6fbc4bb503524f71ceb45)

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

@cncastillo & @mathieuboudreau & @felixhorger, 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 @Kevin-Mattheus-Moerman 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 @cncastillo

📝 Checklist for @felixhorger

📝 Checklist for @mathieuboudreau

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

editorialbot · 2023-09-26T07:30:58Z

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

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

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

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editorialbot · 2023-09-26T07:31:01Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1073.7 files/s, 176673.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           24           1027            915           1941
XSLT                             1             58             30            840
TeX                              1             34              0            473
Markdown                         4             55              0            158
TOML                             1              3              0             96
Bourne Shell                     1              6              1             52
YAML                             3              9             12             49
-------------------------------------------------------------------------------
SUM:                            35           1192            958           3609
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-09-26T07:31:02Z

Wordcount for paper.md is 2231

editorialbot · 2023-09-26T07:31:24Z

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

OK DOIs

- 10.1002/mrm.23217 is OK
- 10.1002/mrm.24263 is OK
- 10.1002/mrm.28554 is OK
- 10.1002/jmri.20320 is OK
- 10.1109/TMI.2002.808360 is OK
- 10.1002/mrm.22767 is OK
- 10.1002/mrm.25827 is OK
- 10.1002/mrm.1241 is OK
- 10.1137/141000671 is OK
- 10.1002/mrm.26089 is OK
- 10.1002/mrm.25841 is OK
- 10.1002/mrm.24389 is OK
- 10.5281/ZENODO.592960 is OK
- 10.1002/mrm.29384 is OK
- 10.1002/mrm.28792 is OK
- 10.1002/mrm.24751 is OK
- 10.1109/TMI.2008.2006526 is OK
- 10.1109/TMI.2008.923956 is OK
- 10.1016/j.mri.2020.06.005 is OK
- 10.1002/mrm.27583 is OK
- 10.1109/TCI.2020.3031082 is OK
- 10.1002/mrm.1910390218 is OK
- 10.5281/zenodo.6510021 is OK
- 10.1002/mrm.27176 is OK
- 10.1016/j.neuroimage.2021.118674 is OK
- 10.1016/j.neuroimage.2017.07.062 is OK
- 10.1016/j.neuroimage.2021.118738 is OK

MISSING DOIs

- 10.58530/2022/2435 may be a valid DOI for title: Open-source model-based reconstruction in Julia: A pipeline for spiral diffusion imaging
- 10.58530/2022/0641 may be a valid DOI for title: MR System Stability and Quality Control using Gradient Impulse Response Functions (GIRF)

INVALID DOIs

- None

cncastillo · 2023-09-26T19:56:46Z

Review checklist for @cncastillo

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/BRAIN-TO/GIRFReco.jl?
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 (@alexjaffray) 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?

cncastillo · 2023-09-26T19:57:37Z

@editorialbot generate pdf

editorialbot · 2023-09-26T19:59:37Z

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

felixhorger · 2023-09-26T20:39:29Z

Review checklist for @felixhorger

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/BRAIN-TO/GIRFReco.jl?
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 (@alexjaffray) 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?

felixhorger · 2023-09-29T12:14:32Z

The DOIs it found for the ISMRM abstracts actually work, amazing, I didn't know about this 👍
@alexjaffray I think it's worth adding them into the .bib

felixhorger · 2023-09-29T15:52:43Z

Please find my comments on the manuscript here: 10.21105.joss.05877_FH.pdf.

The main point I'd like to bring up is that the paper makes it seem like there isn't a clear separation in the code of the (abstract) pipeline itself, reading and writing of data and additional features like plotting. In my opinion there should be a clear separation, outsourcing as much as possible (I'm a fan of an ecosystem of packages rather than a toolbox). This separation would make use more flexible, and adaptation to new scenarios easier (you also mention this point in your paper). How exactly this could look like I'll have to clarify after I read the code in more detail.

Kevin-Mattheus-Moerman · 2023-10-15T06:43:38Z

@alexjaffray could you please respond to the points raised by @felixhorger ?

Kevin-Mattheus-Moerman · 2023-10-15T06:45:16Z

@cncastillo, could you provide an update on review progress? Are there any key issues the authors should work on?

@mathieuboudreau, please can you start your review at this point? You can call @editorialbot generate my checklist to obtain your reviewer checklist.

mathieuboudreau · 2023-10-15T14:05:20Z

Review checklist for @mathieuboudreau

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/BRAIN-TO/GIRFReco.jl?
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 (@alexjaffray) 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?

alexjaffray · 2023-10-17T21:56:01Z

Please find my comments on the manuscript here: 10.21105.joss.05877_FH.pdf.

The main point I'd like to bring up is that the paper makes it seem like there isn't a clear separation in the code of the (abstract) pipeline itself, reading and writing of data and additional features like plotting. In my opinion there should be a clear separation, outsourcing as much as possible (I'm a fan of an ecosystem of packages rather than a toolbox). This separation would make use more flexible, and adaptation to new scenarios easier (you also mention this point in your paper). How exactly this could look like I'll have to clarify after I read the code in more detail.

Thanks for the feedback! Your pdf comments seem to evolve over the course of the document, and you mentioned that you will read the code and clarify some things. Should we start to address your comments, or should we wait until you are finished (preferred)? We are also very happy to address each code review issue dynamically in Github, but likely it would be good to have all reviewers comments and suggestions first so that we don't duplicate work. Would this be alright with you @felixhorger

felixhorger · 2023-10-18T09:07:42Z

@alexjaffray yes I think that's a good idea, there are some minor comments on clarity which could be implemented already so that the other reviewers can proof-read that. The comments on the structure of the code can be left aside for now until all reviewers finished reading the code and gave their opinion.

Kevin-Mattheus-Moerman · 2023-10-18T20:47:42Z

@alexjaffray @felixhorger you may choose the approach that you like. However, usually we see the review progresses fastest/smoothest when the authors respond to issues directly as soon as they come in. This way the reviewers do not have to wait (their issues are being dealt with quickly).

mathieuboudreau · 2023-10-19T03:25:10Z

I started going through the checklist. Here I'll keep a running list issues or PRs in the repo that I've opened and if they've been completed/closed or not yet.

Installation clarity - Add more installation details for users new to Julia BRAIN-TO/GIRFReco.jl#11

cncastillo · 2023-10-19T16:31:06Z

Hi sorry for not replying. I will start to go through the checklist as well.

Just wanted to mention that I had a problem during installation due to a package incompatibility caused by Flux.jl (in an environment with more things that required CUDA). I think this problem it is caused beacuse the Project.toml is a little blaoted. I know (by experience) that this is very annoying to fix, but I think it is necessary.

I also noticed that the package has no tests.

I will leave these issues while I see the rest:

mrikasper · 2023-10-19T21:53:41Z

Dear Felix @felixhorger and Carlos @cncastillo,

I noticed both in Felix' review comment here and one of Carlos' issues a more conceptual question that I wanted to discuss a bit: Both of you are emphasizing the importance of modularization and small packages with limited, but efficient functionality.

I understand the need for that and the elegance in replacing certain tools based on one's specific needs, but in the end, in order to solve a complex task, we have to combine these tools into an elaborate pipeline that needs to make specific choices and adapt to the idiosyncrasies of our use cases. Reconstructing simulated data from a nominal Archimedean spiral is something different than turning real data from a real scanner into images that should then be used in established neuroimaging tools for further analysis, like FSL DTIFIT for diffusion (which rely on NIfTI as input format).

This is what our submission is mainly about (a pipeline for...), in particular GIRFReco.jl, whereas MRIGradients.jl is more of a tool in the sense that you describe it. In other parts of neuroimaging, having complex pipelines standardized and published is definitely seen as valuable, for example fmriprep for functional MRI, and I don't see why image reconstruction would differ in this respect.

Is this maybe a Julia-specific preference? Or because of what the notion of a "package" is in Julia? Originally, our repository was not even a package, but rather a project, and I would say mainly for practical reasons, e.g., ease of installation, we changed this during the pre-review process. It does make sense to have it as a package, I think, because other deployment features also become standardized (e.g., documentation and testing, which you pointed out), but maybe this is where the different expectations come from?

Looking forward to your insights,
Lars

cncastillo · 2023-10-20T03:16:04Z

Dear Lars @mrikasper,

To keep myself from overextending here, I will reply about modularization in BRAIN-TO/GIRFReco.jl#12.

I think there could be a naming issue, as the name of the package GIRFReco.jl gives the impression that it provides the tools to do a GIRF-corrected reconstruction from the user's data (which is conceptually different from the coils sens. and B0 map estimation, IO, etc.). For example, if I want to include the linear gradient self-terms and $k_0$ corrections to my MRF radial data (or spiral), it seems that the most useful package would be MRIGradients.jl, as I could not easily use GIRFReco.jl.

A name that more closely represents what the packages are meant to do (core functionality) is needed to set expectations correctly. For example, MRISpiralDiffusionReco.jl, and MRIGIRFCompensation.jl. Maybe the efforts in documentation, tests, CI, etc, need to go to the package currently named MRIGradients.jl, and the presented pipeline can be an example use case that integrates fancier coils estimation, B0 correction, IO, etc.

Cheers!

felixhorger · 2023-10-22T16:00:09Z

Regarding the reproducibility of original results from the paper: there are phantom and in vivo results. The in vivo results cannot be reproduced by the reviewers due to data protection (see @mrikasper's comment here).
For the phantom results, there is no code available, maybe it makes sense to include that in the joss_example.jl, i.e. to produce exactly the same plot as in the paper on top of the existing ones?

felixhorger · 2023-10-22T16:44:55Z

I reckon this point

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

is implicitly fulfilled because the code is on github, hence anyone can do 1), 2), 3)? Or is an explicit statement required @Kevin-Mattheus-Moerman?

editorialbot · 2024-04-30T11:47:41Z

Done! version is now v0.1.7

Kevin-Mattheus-Moerman · 2024-04-30T11:48:08Z

@editorialbot set 10.5281/zenodo.11075548 as archive

editorialbot · 2024-04-30T11:48:11Z

Done! archive is now 10.5281/zenodo.11075548

Kevin-Mattheus-Moerman · 2024-04-30T11:48:33Z

@editorialbot check references

editorialbot · 2024-04-30T11:51:18Z

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

OK DOIs

- 10.1002/mrm.23217 is OK
- 10.1002/mrm.24263 is OK
- 10.1002/mrm.28554 is OK
- 10.1002/jmri.20320 is OK
- 10.1109/TMI.2002.808360 is OK
- 10.1002/mrm.22767 is OK
- 10.1002/mrm.25827 is OK
- 10.1002/mrm.1241 is OK
- 10.1137/141000671 is OK
- 10.1002/mrm.26089 is OK
- 10.1002/mrm.25841 is OK
- 10.1002/mrm.24389 is OK
- 10.5281/ZENODO.592960 is OK
- 10.1002/mrm.29384 is OK
- 10.1002/mrm.28792 is OK
- 10.1002/mrm.24751 is OK
- 10.1109/TMI.2008.2006526 is OK
- 10.1109/TMI.2008.923956 is OK
- 10.1016/j.mri.2020.06.005 is OK
- 10.1002/mrm.27583 is OK
- 10.1109/TCI.2020.3031082 is OK
- 10.1002/mrm.1910390218 is OK
- 10.5281/zenodo.6510021 is OK
- 10.1002/mrm.27176 is OK
- 10.1016/j.neuroimage.2021.118674 is OK
- 10.1016/j.neuroimage.2017.07.062 is OK
- 10.1016/j.neuroimage.2021.118738 is OK

MISSING DOIs

- No DOI given, and none found for title: Comparison of gradient impulse response functions ...
- 10.58530/2022/2435 may be a valid DOI for title: Open-source model-based reconstruction in Julia: A...
- 10.58530/2022/0641 may be a valid DOI for title: MR System Stability and Quality Control using Grad...
- No DOI given, and none found for title: NIfTI Data Format
- No DOI given, and none found for title: MRI-gradient / GIRF
- No DOI given, and none found for title: Feasibility of Spiral Diffusion Imaging on a Clini...
- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2024-04-30T11:52:47Z

@alexjaffray please can you work on the above potential DOI issues?

alexjaffray · 2024-04-30T13:48:13Z

@Kevin-Mattheus-Moerman the items with no DOI given are correct, there is no DOI available for those 5 items and we have cited them as the authors of the packages/platforms suggest.

Regarding the two items which have a "possibly valid" DOI, the dois suggested are correct but do not link directly to the works. Using the links we provided provides a direct link to those conference abstracts. What would you suggest in this case?

mrikasper · 2024-04-30T17:20:37Z

@alexander: For the two ISMRM Abstracts, I think it's more long-lasting to put the DOI, and the full document is only one click away then. Similar to how most publishers DOIs redirect to the HTML page with the paper abstract, not the full text or pdf. Of course, if there is a second field for URL (besides DOI) you can use the full-text link there. All the best, Lars

…

-- Lars Kasper, PhD (he/him) ***@***.*** MR Physicist Toronto Neuroimaging Facility (ToNI), Department of Psychology, University of Toronto 325 Huron St, Toronto, ON M5S 3J7 phone: +1 416-978-7613 (office) / +1 416-946-0356 (scanner)

________________________________ From: Alexander Jaffray ***@***.***> Sent: Tuesday, April 30, 2024 9:48:35 AM To: openjournals/joss-reviews ***@***.***> Cc: Lars Kasper ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [REVIEW]: GIRFReco.jl: An open-source pipeline for spiral MRI reconstruction in Julia (Issue #5877) @Kevin-Mattheus-Moerman<https://github.com/Kevin-Mattheus-Moerman> the items with no DOI given are correct, there is no DOI available for those 5 items and we have cited them as the authors of the packages/platforms suggest. Regarding the two items which have a "possibly valid" DOI, the dois suggested are correct but do not link directly to the works. Using the links we provided provides a direct link to those conference abstracts. What would you suggest in this case? — Reply to this email directly, view it on GitHub<#5877 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADFUIX7ED2CSKWJCHH2RGXLY76OLHAVCNFSM6AAAAAA5HHT7ZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBVGM4DSNZRHE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

alexjaffray · 2024-05-02T07:17:45Z

@Kevin-Mattheus-Moerman @mrikasper I've added the DOIs for the abstracts which have them (the two suggested above), and pushed to the repository. @Kevin-Mattheus-Moerman Let me know if that is all that's required or if I need to re-archive everything.

Kevin-Mattheus-Moerman · 2024-05-02T08:09:06Z

@editorialbot check references

editorialbot · 2024-05-02T08:09:40Z

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

OK DOIs

- 10.58530/2022/2435 is OK
- 10.58530/2022/0641 is OK
- 10.1002/mrm.23217 is OK
- 10.1002/mrm.24263 is OK
- 10.1002/mrm.28554 is OK
- 10.1002/jmri.20320 is OK
- 10.1109/TMI.2002.808360 is OK
- 10.1002/mrm.22767 is OK
- 10.1002/mrm.25827 is OK
- 10.1002/mrm.1241 is OK
- 10.1137/141000671 is OK
- 10.1002/mrm.26089 is OK
- 10.1002/mrm.25841 is OK
- 10.1002/mrm.24389 is OK
- 10.5281/ZENODO.592960 is OK
- 10.1002/mrm.29384 is OK
- 10.1002/mrm.28792 is OK
- 10.1002/mrm.24751 is OK
- 10.1109/TMI.2008.2006526 is OK
- 10.1109/TMI.2008.923956 is OK
- 10.1016/j.mri.2020.06.005 is OK
- 10.1002/mrm.27583 is OK
- 10.1109/TCI.2020.3031082 is OK
- 10.1002/mrm.1910390218 is OK
- 10.5281/zenodo.6510021 is OK
- 10.1002/mrm.27176 is OK
- 10.1016/j.neuroimage.2021.118674 is OK
- 10.1016/j.neuroimage.2017.07.062 is OK
- 10.1016/j.neuroimage.2021.118738 is OK

MISSING DOIs

- No DOI given, and none found for title: Comparison of gradient impulse response functions ...
- No DOI given, and none found for title: NIfTI Data Format
- No DOI given, and none found for title: MRI-gradient / GIRF
- No DOI given, and none found for title: Feasibility of Spiral Diffusion Imaging on a Clini...
- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox

INVALID DOIs

- None

alexjaffray · 2024-05-02T08:46:26Z

@Kevin-Mattheus-Moerman Thanks for running that again, the references look good to me, the MISSING DOIs list is correct, these are indeed items without dois

Kevin-Mattheus-Moerman · 2024-05-02T09:55:10Z

@editorialbot recommend-accept

editorialbot · 2024-05-02T09:55:13Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-05-02T09:55:58Z

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

OK DOIs

- 10.58530/2022/2435 is OK
- 10.58530/2022/0641 is OK
- 10.1002/mrm.23217 is OK
- 10.1002/mrm.24263 is OK
- 10.1002/mrm.28554 is OK
- 10.1002/jmri.20320 is OK
- 10.1109/TMI.2002.808360 is OK
- 10.1002/mrm.22767 is OK
- 10.1002/mrm.25827 is OK
- 10.1002/mrm.1241 is OK
- 10.1137/141000671 is OK
- 10.1002/mrm.26089 is OK
- 10.1002/mrm.25841 is OK
- 10.1002/mrm.24389 is OK
- 10.5281/ZENODO.592960 is OK
- 10.1002/mrm.29384 is OK
- 10.1002/mrm.28792 is OK
- 10.1002/mrm.24751 is OK
- 10.1109/TMI.2008.2006526 is OK
- 10.1109/TMI.2008.923956 is OK
- 10.1016/j.mri.2020.06.005 is OK
- 10.1002/mrm.27583 is OK
- 10.1109/TCI.2020.3031082 is OK
- 10.1002/mrm.1910390218 is OK
- 10.5281/zenodo.6510021 is OK
- 10.1002/mrm.27176 is OK
- 10.1016/j.neuroimage.2021.118674 is OK
- 10.1016/j.neuroimage.2017.07.062 is OK
- 10.1016/j.neuroimage.2021.118738 is OK

MISSING DOIs

- No DOI given, and none found for title: Comparison of gradient impulse response functions ...
- No DOI given, and none found for title: NIfTI Data Format
- No DOI given, and none found for title: MRI-gradient / GIRF
- No DOI given, and none found for title: Feasibility of Spiral Diffusion Imaging on a Clini...
- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox

INVALID DOIs

- None

editorialbot · 2024-05-02T09:57:20Z

👋 @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#5295, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-05-02T10:03:26Z

@alexjaffray it looks like we are good to proceed. However, I would add one minor comment. On the Zenodo archive listing the spelling for the author Kâmil Uludağ does not feature the special characters. It may be good to edit this person's name there to match how it is listed in the paper too. You can do as if you wish but we can proceed to process this for acceptance at this point.

Kevin-Mattheus-Moerman · 2024-05-02T10:03:39Z

@editorialbot accept

editorialbot · 2024-05-02T10:03:41Z

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

editorialbot · 2024-05-02T10:10:21Z

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: Jaffray
  given-names: Alexander
  orcid: "https://orcid.org/0000-0002-9571-1838"
- family-names: Wu
  given-names: Zhe
  orcid: "https://orcid.org/0000-0002-2079-5977"
- family-names: Vannesjo
  given-names: S. Johanna
  orcid: "https://orcid.org/0000-0003-2432-4192"
- family-names: Uludağ
  given-names: Kâmil
  orcid: "https://orcid.org/0000-0002-2813-5930"
- family-names: Kasper
  given-names: Lars
  orcid: "https://orcid.org/0000-0001-7667-603X"
contact:
- family-names: Jaffray
  given-names: Alexander
  orcid: "https://orcid.org/0000-0002-9571-1838"
- family-names: Wu
  given-names: Zhe
  orcid: "https://orcid.org/0000-0002-2079-5977"
doi: 10.5281/zenodo.11075548
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jaffray
    given-names: Alexander
    orcid: "https://orcid.org/0000-0002-9571-1838"
  - family-names: Wu
    given-names: Zhe
    orcid: "https://orcid.org/0000-0002-2079-5977"
  - family-names: Vannesjo
    given-names: S. Johanna
    orcid: "https://orcid.org/0000-0003-2432-4192"
  - family-names: Uludağ
    given-names: Kâmil
    orcid: "https://orcid.org/0000-0002-2813-5930"
  - family-names: Kasper
    given-names: Lars
    orcid: "https://orcid.org/0000-0001-7667-603X"
  date-published: 2024-05-02
  doi: 10.21105/joss.05877
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5877
  title: "GIRFReco.jl: An Open-Source Pipeline for Spiral Magnetic
    Resonance Image (MRI) Reconstruction in Julia"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05877"
  volume: 9
title: "GIRFReco.jl: An Open-Source Pipeline for Spiral Magnetic
  Resonance Image (MRI) Reconstruction in Julia"

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.

Find more information on .cff files here and here.

editorialbot · 2024-05-02T10:10:24Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-05-02T10:10:25Z

🚨🚨🚨 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.05877 joss-papers#5296
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05877
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

alexjaffray · 2024-05-02T21:53:13Z

@Kevin-Mattheus-Moerman Everything looks good, and the DOI resolves! Thank you!

Kevin-Mattheus-Moerman · 2024-05-03T07:04:57Z

@alexjaffray great. Well done and congratulations on this JOSS publication!

And a special thanks to the fantastic reviewers!!! @cncastillo, @mathieuboudreau, @felixhorger

editorialbot · 2024-05-03T07:04:59Z

🎉🎉🎉 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://joss.theoj.org/papers/10.21105/joss.05877/status.svg)](https://doi.org/10.21105/joss.05877)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05877">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05877/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05877/status.svg
   :target: https://doi.org/10.21105/joss.05877

This is how it will look in your documentation:

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editorialbot added Julia review Shell Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials XSLT labels Sep 26, 2023

editorialbot assigned Kevin-Mattheus-Moerman Sep 26, 2023

editorialbot mentioned this issue Sep 26, 2023

[PRE REVIEW]: GIRFReco.jl: An open-source pipeline for spiral MRI reconstruction in Julia #5515

Closed

felixhorger mentioned this issue Sep 30, 2023

Config files and root directory BRAIN-TO/GIRFReco.jl#9

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 2, 2024

editorialbot added accepted published Papers published in JOSS labels May 2, 2024

Kevin-Mattheus-Moerman closed this as completed May 3, 2024

editorialbot mentioned this issue Nov 19, 2024

[PRE REVIEW]: MRI-NUFFT: Doing non-Cartesian MRI has never been easier #7501

Open

[REVIEW]: GIRFReco.jl: An open-source pipeline for spiral MRI reconstruction in Julia #5877

[REVIEW]: GIRFReco.jl: An open-source pipeline for spiral MRI reconstruction in Julia #5877

Comments

editorialbot commented Sep 26, 2023 • edited Loading

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Reviewer instructions & questions

Checklists

editorialbot commented Sep 26, 2023

editorialbot commented Sep 26, 2023

editorialbot commented Sep 26, 2023

editorialbot commented Sep 26, 2023

cncastillo commented Sep 26, 2023 • edited Loading

Review checklist for @cncastillo

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

cncastillo commented Sep 26, 2023

editorialbot commented Sep 26, 2023

felixhorger commented Sep 26, 2023 • edited Loading

Review checklist for @felixhorger

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

felixhorger commented Sep 29, 2023

felixhorger commented Sep 29, 2023

Kevin-Mattheus-Moerman commented Oct 15, 2023

Kevin-Mattheus-Moerman commented Oct 15, 2023

mathieuboudreau commented Oct 15, 2023 • edited Loading

Review checklist for @mathieuboudreau

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

alexjaffray commented Oct 17, 2023

felixhorger commented Oct 18, 2023

Kevin-Mattheus-Moerman commented Oct 18, 2023

mathieuboudreau commented Oct 19, 2023 • edited Loading

cncastillo commented Oct 19, 2023 • edited Loading

mrikasper commented Oct 19, 2023

cncastillo commented Oct 20, 2023 • edited Loading

felixhorger commented Oct 22, 2023

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alexjaffray commented May 2, 2024 • edited Loading

Kevin-Mattheus-Moerman commented May 3, 2024

editorialbot commented May 3, 2024

editorialbot commented Sep 26, 2023 •

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cncastillo commented Sep 26, 2023 •

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felixhorger commented Sep 26, 2023 •

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mathieuboudreau commented Oct 15, 2023 •

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