[REVIEW]: pypulseq: A Python Package for MRI Pulse Sequence Design

[whedon]

Submitting author: @imr-framework (Sairam Geethanath)
Repository: https://github.com/imr-framework/pypulseq
Version: 1.2.2r1
Editor: @Kevin-Mattheus-Moerman
Reviewers: @grlee77, @mathieuboudreau, @spinicist
Archive: 10.5281/zenodo.3479527

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Review checklist for @grlee77

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General checks

• Repository: Is the source code for this software available at the repository url?
• 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 (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
• 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?

Review checklist for @mathieuboudreau

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• 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 (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
• 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?

Review checklist for @spinicist

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• 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 (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @grlee77, @mathieuboudreau it looks like you're currently assigned to review this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[Kevin-Mattheus-Moerman]

@imr-framework, @grlee77, @mathieuboudreau this is where the review takes place. The reviewers each have a set of tick boxes at the top of this issue to guide them through the process. Let me know if you have any questions. Let the reviewing begin!

[Kevin-Mattheus-Moerman]

@whedon add @spinicist as reviewer

[whedon]

OK, @spinicist is now a reviewer

[Kevin-Mattheus-Moerman]

Thanks for joining @spinicist, I've added a checkbox set for you at the top

[grlee77]

I have performed my initial review.

Summary

The Pypulseq software is a port of the Pulseq Matlab package to Python. This makes the Pulseq format for rapid sequence prototyping more readily available to sites without need for a commercial license. The authors also have used Python-based machine learning in combination with Pypulseq for novel sequence design. The overall goal is to have a tool for rapid sequence development without relying on complicated and proprietary vendor-specific pulse sequence development tools. The advantage of such an approach is greatly reduced development time for simple experiments and rapid prototyping.

I verified that Pulseq files are produced by running the examples. The generated files are plain text and appear to conform to the Pulseq specification. I currently work with Philips MR systems, which is not one of the supported vendors, so I did not attempt to verify proper execution of the Pulseq files on a physical MRI scanner.

The software appears to work as advertised. Its main weakness in relation to the JOSS criteria is the lack of automated testing and/or continuous integration to test across platforms. I opened imr-framework/pypulseq#16 regarding this.

Comments regarding the text of the paper

1.) A brief statement on the limitations of the types of sequences that can be designed with this simplified approach is warranted so as not to oversell the capabilities. For example, it seems that scans requiring features such as cardiac or respiratory gating, feedback from real-time image-based navigators, etc. are not going to be possible. I assume that it also presents difficulty for scans that require more complicated planning such as placement of saturation slabs and or localized shim boxes interactively prior to scan start.

2.) Similarly, is offline image reconstruction (i.e. not with the vendor-supplied reconstructor) always required when using this tool?

3.) I would add a reference to J. Nielsen's TOPPE publication as a closely related work (https://doi.org/10.1002/mrm.26990). (It seems that on the GE platform a Pulseq->TOPPE conversion is done to actually play out the sequences on the scanner?).

4.) For the puposes of the "state of the field" JOSS criteria, it should probably also be mentioned how this framework (and TOPPE) are fast and do not require compilation (as compared to C++ frameworks like ODIN or SequenceTree).

5.) Are there any areas that pypulseq currently offers additional functionality (or lacks functionality) relative to the Matlab implementation? This would be good to know for existing Matlab users thinking of making the switch to Python.

Minor typos/suggested phrasing changes

1.) in the summary:
"easy integrability with" -> "easy integration with"

2.) under the "Statement of Need"
"These are aimed at achieving" <- unclear what "these" is referring to

3.) in the section on the Pulseq format:

"A pulse sequence comprises of pulsed, magnetic field gradient, delay or ADC readout events" ->

"A pulse sequence comprises of radiofrequency pulses, magnetic field gradient waveforms, delays or analog-to-digital converter (ADC) readout events"

4.) Please include the meeting names (International Society for Magnetic Resonance in Medicine?) for the fourth reference and last reference.

[sravan953]

@grlee77 Thank you for your comments, will work on them and revert. Have a nice weekend!

[sravan953]

@grlee77 I have addressed your comments in the most recent commit. Please take a look!

More specifically regarding #5 in your comments: our future efforts involve incorporating SAR computation and real-time pulse sequence design.

[mathieuboudreau]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[mathieuboudreau]

Contribution and authorship: Has the submitting author (@imr-framework) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

@imr-framework could you clarify what contribution(s) John Thomas Vaughan Jr. made to this project; I checked out the contributors to the source code here, and he doesn't appear on the list (whereas @tonggehua has made some commits and doesn't appear on the paper).

[mathieuboudreau]

@imr-framework does there exist some kind of validator tool to evaluate if a generated *.seq file is (1) properly formatted, and (2) doesn't exceed vendor-imposed hardware limits. I don't expect that this exists within your software, since *.seq files have been developed previously, I'm wondering if there's an external tool that already does this?

[sravan953]

@mathieuboudreau
Regarding contributions-
John Thomas Vaughan Jr. has been principally involved in the design and review of this project, like for Virtual Scanner. We have been using PyPulseq internally, and the one commit from @tonggehua was regarding documentation. The authors list was finalised after internal deliberations.

Regarding the formatting-
We utilised a diffcheck tool to ensure that the *.seq files generated by PyPulseq match with Pulseq 1.2.0's files. We performed these checks for the demo scripts that have been bundled. The only difference between *.seq files generated by PyPulseq and Pulseq 1.2.0 is the comment on line 2 in every *.seq file which indicates which tool generated the file.

Regarding an external validator tool-
The check_timing() and test_report() methods can be leveraged to ensure that the designed pulse sequence is in accordance with the specified gradient raster time limits. Subsequently, a successfully generated *.seq file might or might not play on the scanner, depending on whether the hardware limits were violated or not.

[mathieuboudreau]

Ok great, thanks for all that additional information!

[whedon]

OK. 1.2.2r1 is the version.

[Kevin-Mattheus-Moerman]

@whedon set 10.5281/zenodo.3479527 as archive

[whedon]

OK. 10.5281/zenodo.3479527 is the archive.

[Kevin-Mattheus-Moerman]

@openjournals/joss-eics I recommend this paper for acceptance in JOSS.

@sravan953 the editor in chief on call will take over now. They might have additional comments on your paper.

[Kevin-Mattheus-Moerman]

@sravan953 one last point from me. I would recommend that you update your paper title (and also the matched Zenodo archive title) to be a bit more descriptive, e.g.:
PyPulseq: A Python Package for MRI Pulse Sequence Design
Something like that would help make your paper more discoverable.
@arfon is this something that we can change just in the PDF or do we need to propagate the title change anywhere else?

[arfon]

@arfon is this something that we can change just in the PDF or do we need to propagate the title change anywhere else?

Just the paper.md should do it.

[sravan953]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[sravan953]

@Kevin-Mattheus-Moerman @arfon Updated the title on the README.md, Zenodo archive and on paper.md.

[labarba]

I fixed in-text citation syntax and a terminology issue in imr-framework/pypulseq#23

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1002/mrm.26235 is OK
- 10.1016/j.mri.2018.03.008 is OK
- 10.1016/j.jmr.2004.05.021 is OK
- 10.1002/mrm.25640 is OK
- 10.1002/mrm.26990 is OK
- 10.1615/CritRevBiomedEng.2019029380 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1023

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1023, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[labarba]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01725 joss-papers#1024
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01725
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[labarba]

Congratulations, @imr-framework, your JOSS paper is published! 🚀

Huge thanks to our editor: @Kevin-Mattheus-Moerman, and the reviewers: @grlee77, @mathieuboudreau, @spinicist — your contributions to JOSS are greatly appreciated 🙏

[whedon]

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

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[sairamgeethanath]

Congratulations, @imr-framework, your JOSS paper is published! 🚀

Huge thanks to our editor: @Kevin-Mattheus-Moerman, and the reviewers: @grlee77, @mathieuboudreau, @spinicist — your contributions to JOSS are greatly appreciated 🙏

Many thanks to all the reviewers @mathieuboudreau @spinicist @grlee77, the editor @Kevin-Mattheus-Moerman and the associate editor in chief @labarba for the time and inputs to make our work better.