[PRE REVIEW]: PyGRASP: A library to reconstruct dynamic contrast enhanced MR images acquired with radial sampling

[editorialbot]

Submitting author: !--author-handle-->@cariyurek<!--end-author-handle-- (Cemre Ariyurek) Repository: https://github.com/quin-med-harvard-edu/pyGRASP Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @kerkelae, @curtcorum Managing EiC: Daniel S. Katz

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Author instructions

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

@cariyurek 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

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[editorialbot]

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:

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

@editorialbot generate pdf

[editorialbot]

Couldn't check the bibtex because branch name is incorrect: https://github.com/quin-med-harvard-edu/pyGRASP/blob/main/paper.md

[editorialbot]

Couldn't check the bibtex because branch name is incorrect: https://github.com/quin-med-harvard-edu/pyGRASP/blob/main/paper.md

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (422.5 files/s, 49539.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            384            535           1467
YAML                             2              1              0            249
Markdown                         2             66              0            204
TeX                              1             12              0            125
JSON                             2              1              0            100
Bourne Shell                     2              7              0             15
-------------------------------------------------------------------------------
SUM:                            27            471            535           2160
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1672

[editorialbot]

Failed to discover a Statement of need section in paper

[danielskatz]

@editorialbot check references

[danielskatz]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

@cariyurek - I'm not sure exactly what the problem is here. You might want to try removing the blank lines in your paper's metadata section and more closely following the JOSS example paper. Also, your paper needs a "Statement of Need" section. Then use the command @editorialbot generate pdf to try to make the PDF. editorialbot commands need to be the first entry in a new comment.

[cariyurek]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cariyurek]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cariyurek]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cariyurek]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[cariyurek]

@editorialbot generate pdf

[editorialbot]

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

[danielskatz]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX entry: cite-key missing

[danielskatz]

@cariyurek - can you try removing the blank link in a bib entry (line 24) in your bib file, then try this command again?

[danielskatz]

Also, we don't currently have any appropriate editors with availability for additional papers, so I'm going to put this on our waitlist for now.

[cariyurek]

@editorialbot generate pdf

[editorialbot]

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

[cariyurek]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.6084/m9.figshare.20465637.v1 is OK

MISSING DOIs

- 10.1002/mrm.22446 may be a valid DOI for title: 3D undersampled golden-radial phase encoding for DCE-MRA using inherently regularized iterative SENSE
- 10.1002/mrm.22453 may be a valid DOI for title: Nonlinear inverse reconstruction for real-time MRI of the human heart using undersampled radial FLASH
- 10.1002/mrm.22172 may be a valid DOI for title: Radial k-t FOCUSS for high-resolution cardiac cine MRI
- 10.1002/mrm.24980 may be a valid DOI for title: Golden-angle radial sparse parallel MRI: Combination of compressed sensing, parallel imaging, and golden-angle radial sampling for fast and flexible dynamic volumetric MRI
- 10.1002/jmri.27021 may be a valid DOI for title: Bulk motion-compensated DCE-MRI for functional imaging of kidneys in newborns
- 10.1016/j.media.2020.101880 may be a valid DOI for title: Modeling dynamic radial contrast enhanced MRI with linear time invariant systems for motion correction in quantitative assessment of kidney function

INVALID DOIs

- None

[cariyurek]

@editorialbot generate pdf

[editorialbot]

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

[cariyurek]

@danielskatz Thank you. I believe I have fixed the bib file now.

[danielskatz]

@editorialbot check references

let's find out :)

[editorialbot]

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

OK DOIs

- 10.6084/m9.figshare.20465637.v1 is OK

MISSING DOIs

- 10.1002/mrm.22446 may be a valid DOI for title: 3D undersampled golden-radial phase encoding for DCE-MRA using inherently regularized iterative SENSE
- 10.1002/mrm.22453 may be a valid DOI for title: Nonlinear inverse reconstruction for real-time MRI of the human heart using undersampled radial FLASH
- 10.1002/mrm.22172 may be a valid DOI for title: Radial k-t FOCUSS for high-resolution cardiac cine MRI
- 10.1002/mrm.24980 may be a valid DOI for title: Golden-angle radial sparse parallel MRI: Combination of compressed sensing, parallel imaging, and golden-angle radial sampling for fast and flexible dynamic volumetric MRI
- 10.1002/jmri.27021 may be a valid DOI for title: Bulk motion-compensated DCE-MRI for functional imaging of kidneys in newborns
- 10.1016/j.media.2020.101880 may be a valid DOI for title: Modeling dynamic radial contrast enhanced MRI with linear time invariant systems for motion correction in quantitative assessment of kidney function

INVALID DOIs

- None

[danielskatz]

Please check 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 when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[cariyurek]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/TMI.2015.2509245 is OK
- 10.1002/mrm.22446 is OK
- 10.1002/mrm.22453 is OK
- 10.1002/mrm.22172 is OK
- 10.1002/mrm.24980 is OK
- 10.1002/jmri.27021 is OK
- 10.1016/j.media.2020.101880 is OK
- 10.6084/m9.figshare.20465637.v1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[cariyurek]

@editorialbot generate pdf

[editorialbot]

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

[cariyurek]

@editorialbot generate pdf

[editorialbot]

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

[oliviaguest]

@emdupre do you have capacity/time for this?

[emdupre]

Thanks for the invitation, @oliviaguest ! Yes, I should be able to edit this submission 🙂

[emdupre]

@editorialbot assign @emdupre as editor

[editorialbot]

Assigned! @emdupre is now the editor

[emdupre]

👋 Hi @cariyurek, and thank you for your submission to JOSS !

If you have any suggestions for potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here.

You can suggest reviewers from any relevant project, though we often recommend starting with this list of people as they have already agreed to review for JOSS (please start at the bottom of the list).

[cariyurek]

Hi @emdupre ,

We are grateful for your time in considering and reviewing our submission. We do not have any strong suggestions for potential reviewers but looking into the list provided we can suggest curtcorum, kerkelae, spinicist or agahkarakuzu (who is not on the list but has published in JOSS).