[PRE REVIEW]: Lo-Fi-Sim: A python-based open-source platform for image simulation and generation of point-of-care low-field (Lo-Fi) MRI

[editorialbot]

Submitting author: @mathieumach (Mathieu Mach)
Repository: https://github.com/mathieumach/Lo-Fi-Sim
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

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[editorialbot]

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

✅ OK DOIs

- 10.11604/pamj.2018.30.240.14000 is OK
- 10.1002/jmri.26638 is OK
- 10.1002/nbm.4846 is OK
- 10.21105/joss.01637 is OK
- 10.1016/j.jmr.2017.05.007 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Corsmed - MRI Simulator
- No DOI given, and none found for title: IACI MRI Simulation Software \textbar Psychology S...
- No DOI given, and none found for title: ScanLabMR – MRI Training, Education, and Simulator...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (166.5 files/s, 154262.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17           2291           1932          14928
TeX                              1              8              0            113
Markdown                         2             62              0             95
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                            21           2362           1936          15155
-------------------------------------------------------------------------------

Commit count by author:

    35	mathieu mach

[editorialbot]

⚠️ An error happened when generating the pdf. Author (Andrew Webb) is missing affiliation.

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1189

🔴 Failed to discover a Statement of need section in paper

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[mathieumach]

Hello @Kevin-Mattheus-Moerman, thanks for regenerating my paper. It is my first time submitting to JOSS and I am a little lost regarding the next steps of the reviewing process, should I find reviewers from the list on the first message of the editorial bot, or should I contact people from the 5 papers mentioned in the previous editorial bot message? Thanks a lot!

[Kevin-Mattheus-Moerman]

@mathieumach I'm the AEiC on this track. Our website tells us more about the review process. The next steps are that I'll do some checks to see if this is in scope for JOSS. If so, I'll look for a handling editor. Once we have a handling editor then that editor will look for reviewers. So no steps are required yet from your side.

[mathieumach]

@Kevin-Mattheus-Moerman, thank you for your reply and explanations. I will wait for the reviewers and please don’t hesitate to let me know if anything is needed. Have a good day :)

[Kevin-Mattheus-Moerman]

@mathieumach apologies my phone added several typos in my previous message. I've edited it just now, but I think you understood.

[Kevin-Mattheus-Moerman]

@mathieumach some points needing your attention below:

• Can you please clarify the organisation of your repository and the code to me. Usually Python projects feature dedicated folders containing: 1) the source for the core functionality, 2) testing, 3) documentation. With your project it looks like all functional codes are simply in the main folder. I think it would be better to adopt the more usual project organisation.
• Does the project feature automated testing?
• Is all functionality presented here integrated in GUI codes or is functionality separately available (and callable by the GUIs) too?
• On the GUI aspects, we get some submissions whereby GUI related code was created with the help of a dedicated tool for making GUIs. Can you explain if any such tool was used here or if all code can be assumed to be hand written by the authors? If a tool was used, please explain what aspects of the code were manually created by the authors and which were tool generated.
• I see that in your paper you list the references yourself at the end. Please remove this text. Our paper compilation adds all cited content at the end under references anyway. So please remove the numbered list and use normal citations in the text. Note that you can also create bib file entries, and therefore citations, for hyperlinks etc.

[mathieumach]

@Kevin-Mattheus-Moerman Thank you for the points you raised.

• We acknowledge that the current structure of our repository may not fully align with the standard Python project organization. We will revise the repository to adhere to the standard structure with a src folder for the core functionality, a tests folder with files used for testing, and a docs folder with the documentation.
• The current version of the project does not feature automated testing, but different files will be created and added to the tests folder with explanations on how to use these files with the GUI to test the importation of files in the GUI.
• I'm not completely sure I fully understand the question, but most of the functionalities are built into the GUI code. The ones that are separately available and called by the GUI are the analytical equations of the MRI sequences (in the Sequences.py file) and the interactive plots (interactiveAxesPlot_XXX.py files).
• The GUI code was entirely written by the authors with the Tkinter library and without using any GUI design tools (like PyQt Designer or similar). All interface elements, event handling, and layout designs were manually coded.
• Thank you for pointing out the issue with the references section. We will remove the numbered reference list from the end of the paper, and instead, we will use inline citations in the format required by the journal.

[mathieumach]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.7604

PyPulseq: A Python Package for MRI Pulse Sequence Design
Submitting author: @imr-framework
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mathieuboudreau, @spinicist
Similarity score: 0.7556

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7525

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
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Similarity score: 0.7359

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[mathieumach]

@Kevin-Mattheus-Moerman, the organisation of the repository has been modified as you suggested. Please let me know if you need anything from my side before having a handling editor and reviewers. Have a good weekend.

[Kevin-Mattheus-Moerman]

@mathieumach thanks for working on my feedback. I still feel the project/repository organisation is not up to the usual standard. Detailed functional GUI documentation, code documentation, contributing guidelines, and testing appear to be lacking, and the README is not detailed enough (e.g. the missing aspects should be linked to). As it stands this work does not pass our substantial scholarly effort criteria. I would suggest you consider to resubmit when the package is more mature. If unit testing, automated testing, and detailed documentation (and the above aspects) are added we may reconsider this submission. For the moment I'll reject this submission.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.

[mathieumach]

@Kevin-Mattheus-Moerman , I apologize for my late response. Thank you for taking the time to review my submission and for providing detailed and constructive feedback. I sincerely appreciate your thorough assessment and the suggestions for improvement. As I work on addressing the areas you highlighted, I would be grateful for any further advice you could offer regarding the best practices regarding the project repository structure to ensure it meets the usual standards. Once these revisions are completed, I hope to resubmit a more mature and well-documented version of the project for reconsideration.
Have a good day.