[PRE REVIEW]: Open-Source MRI Pulse Sequences with Minimal Echo Times

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@tonggehua<!--end-author-handle-- (Gehua Tong) Repository: https://github.com/imr-framework/minTE Branch with paper.md (empty if default branch): Version: 1.0 Editor: Pending Reviewers: Pending Managing EiC: Daniel S. Katz

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a24dd39878bf549f08805fd54d2c41aa"><img src="https://joss.theoj.org/papers/a24dd39878bf549f08805fd54d2c41aa/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a24dd39878bf549f08805fd54d2c41aa/status.svg)](https://joss.theoj.org/papers/a24dd39878bf549f08805fd54d2c41aa)

Author instructions

Thanks for submitting your paper to JOSS @tonggehua. Currently, there isn't an JOSS editor assigned to your paper.

@tonggehua if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

editorialbot commented 2 years ago

Hello human, 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:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/mrm.26235 is OK
- 10.1016/j.mri.2018.03.008 is OK

MISSING DOIs

- 10.1002/mrm.23026 may be a valid DOI for title: Short echo-time 3D radial gradient-echo MRI using concurrent dephasing and excitation
- 10.1016/j.jmr.2006.05.014 may be a valid DOI for title: Fast and quiet MRI using a swept radiofrequency
- 10.1002/jmri.25708 may be a valid DOI for title: Advances in MRI around metal
- 10.21105/joss.01725 may be a valid DOI for title: PyPulseq: A python package for mri pulse sequence design
- 10.1002/(sici)1522-2594(199903)41:3<591::aid-mrm23>3.0.co;2-r may be a valid DOI for title: Ultra-short echo-time 2D time-of-flight MR angiography using a half-pulse excitation
- 10.1016/j.radi.2004.07.007 may be a valid DOI for title: MR imaging with ultrashort TE (UTE) pulse sequences: Basic principles
- 10.1109/tsp.2002.807005 may be a valid DOI for title: Nonuniform fast Fourier transforms using min-max interpolation
- 10.3390/jimaging4030051 may be a valid DOI for title: Python non-uniform fast Fourier transform (PyNUFFT): An accelerated non-Cartesian MRI package on a heterogeneous platform (CPU/GPU)
- 10.1016/j.mri.2018.03.008 may be a valid DOI for title: Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development
- 10.1002/9781118633953.ch14 may be a valid DOI for title: Projection Reconstruction of Images
- 10.1002/mrm.1910210210 may be a valid DOI for title: Spoiling of transverse magnetization in steady-state sequences
- 10.1002/mrm.26990 may be a valid DOI for title: TOPPE: A framework for rapid prototyping of MR pulse sequences
- 10.1002/jmri.26638 may be a valid DOI for title: Accessible magnetic resonance imaging: A review
- 10.1016/j.mri.2021.11.014 may be a valid DOI for title: A framework for validating open-source pulse sequences
- 10.21105/joss.01637 may be a valid DOI for title: Virtual Scanner: MRI on a Browser
- 10.1016/j.jmr.2011.09.023 may be a valid DOI for title: A k-space analysis of small-tip-angle excitation
- 10.1016/j.mri.2021.11.014 may be a valid DOI for title: A framework for validating open-source pulse sequences
- 10.1002/(sici)1522-2594(199903)41:3<591::aid-mrm23>3.0.co;2-r may be a valid DOI for title: Ultra-short echo-time 2D time-of-flight MR angiography using a half-pulse excitation

INVALID DOIs

- None

editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=25.68 s (1.2 files/s, 125.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            421            705           1311
Markdown                         7            116              0            322
TeX                              1             33              0            249
YAML                             2              3              7             47
Jupyter Notebook                 1              0              1              0
-------------------------------------------------------------------------------
SUM:                            31            573            713           1929
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1270

editorialbot commented 2 years ago

:warning: An error happened when generating the pdf.

danielskatz commented 2 years ago

👋 @tonggehua - Your paper does not compile. Please follow the example paper. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Note that the error link above includes

Problem with affiliations for Gehua Tong, perhaps the affiliations index need quoting?

tonggehua 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:

tonggehua commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @tonggehua, 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

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

tonggehua 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:

tonggehua commented 2 years ago

@danielskatz Thanks for the reminder. The paper now compiles and the missing DOIs have been added.

arfon commented 2 years ago

@editorialbot query scope

@tonggehua – I've noticed that there are a fair number of sections in your code where the logic has been commented out which raises a concern on my side that this submission might not be ready to go out for review yet. I'm querying the scope here to seek the input of a few of our editors. This process will likely take a week or so.

editorialbot commented 2 years ago

Submission flagged for editorial review.

danielskatz 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

- 10.1002/mrm.23026 is OK
- 10.1002/mrm.26235 is OK
- 10.1016/j.mri.2018.03.008 is OK
- 10.1016/j.jmr.2006.05.014 is OK
- 10.1002/jmri.25708 is OK
- 10.21105/joss.01725 is OK
- 10.1002/jmri.27208 is OK
- 10.1016/j.radi.2004.07.007 is OK
- 10.3389/fendo.2020.555756 is OK
- 10.1109/tsp.2002.807005 is OK
- 10.3390/jimaging4030051 is OK
- 10.1016/j.mri.2018.03.008 is OK
- 10.1002/9781118633953.ch14 is OK
- 10.1002/mrm.1910210210 is OK
- 10.1002/mrm.26990 is OK
- 10.1002/jmri.26638 is OK
- 10.1016/j.mri.2021.11.014 is OK
- 10.1101/2021.12.27.474259 is OK
- 10.1016/j.neuroimage.2019.116335 is OK
- 10.21105/joss.01637 is OK
- 10.1016/0022-2364(89)90265-5 is OK
- 10.1002/(sici)1522-2594(199903)41:3<591::aid-mrm23>3.0.co;2-r is OK

MISSING DOIs

- None

INVALID DOIs

- None

tonggehua commented 2 years ago

@arfon What is the timeline for starting the review process?

Many thanks, Gehua

arfon commented 2 years ago

@tonggehua – apologies for the delayed response here. We've struggled to get editor feedback on this submission.

In summary, we have some concerns about sending this submission out for review for a number of reasons:

There are a fair number of sections in your code where the logic has been commented out which raises concerns that this submission might not be ready to go out for review yet.
The paper could use some work to make it more clear to non-experts what problems this code addresses.
The submission seems to be more of a collection of scripts (e.g., https://github.com/imr-framework/minTE/blob/main/minTE/sequences/write_UTE_2D.py) that should be run end-to-end rather than a software package (e.g., with classes, modules, methods) that would meet our submission requirements.

danielskatz commented 2 years ago

@tonggehua - I'm sorry to say that after discussion amongst the JOSS editors, we have decided that we will not review this software at this time.

In addition to the comments from @arfon ☝️ , some other editor comments include:

A relatively small amount of code, and the code seems to come largely from a single contributor in a short amount of time.
It is unclear if this is a large or minor advance over prior developments
For someone coming from slight outside the field, it's hard to understand what the software actually does and why it's important, after reading the README and the submitted paper.

Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your work.

danielskatz commented 2 years ago

@editorialbot reject

editorialbot commented 2 years ago

Paper rejected.

openjournals / joss-reviews

[PRE REVIEW]: Open-Source MRI Pulse Sequences with Minimal Echo Times #4454

Status