[PRE REVIEW]: PET2BIDS: a library for converting Positron Emission Tomography data to BIDS #5822

editorialbot · 2023-09-10T07:38:45Z

Submitting author: @CPernet (Cyril Pernet)
Repository: https://github.com/openneuropet/PET2BIDS/
Branch with paper.md (empty if default branch): JOSS_paper
Version: v1
Editor: @britta-wstnr
Reviewers: @nbeliy, @adswa, @pjtoussaint
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f044fa1d888de6646a8e8dfd5931d0da"><img src="https://joss.theoj.org/papers/f044fa1d888de6646a8e8dfd5931d0da/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f044fa1d888de6646a8e8dfd5931d0da/status.svg)](https://joss.theoj.org/papers/f044fa1d888de6646a8e8dfd5931d0da)

Author instructions

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

@CPernet if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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

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

editorialbot · 2023-09-10T07:38:46Z

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 · 2023-09-10T07:38:53Z

Wordcount for paper.md is 789

editorialbot · 2023-09-10T07:38:54Z

Failed to discover a valid open source license

editorialbot · 2023-09-10T07:38:56Z

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

OK DOIs

- 10.1038/s41597-022-01164-1 is OK
- 10.1016/j.neuroimage.2015.05.049 is OK
- 10.3389/fninf.2011.00037 is OK
- 10.1385/ni:5:1:11 is OK
- 10.1177/0271678X20905433 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
- 10.5281/zenodo.7795644 is OK

MISSING DOIs

- 10.1038/sdata.2016.44 may be a valid DOI for title: The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments
- 10.3389/fninf.2021.770608 may be a valid DOI for title: BIDScoin: A User-Friendly Application to Convert Source Data to Brain Imaging Data Structure

INVALID DOIs

- None

editorialbot · 2023-09-10T07:40:03Z

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

Kevin-Mattheus-Moerman · 2023-09-11T12:53:59Z

@editorialbot set main as branch

editorialbot · 2023-09-11T12:54:01Z

Done! branch is now main

Kevin-Mattheus-Moerman · 2023-09-11T12:54:10Z

@editorialbot check repository

editorialbot · 2023-09-11T12:54:16Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.24 s (404.9 files/s, 88068.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           27           1270           1846           4803
JSON                             12             11              0           4705
MATLAB                           20            498           1212           4023
Markdown                         16            256              0            725
YAML                              6             56             19            306
reStructuredText                  8            258            271            302
Bourne Shell                      1             23            100            269
Ruby                              1             28             12            106
TOML                              1              6              0             52
Bourne Again Shell                3             12             10             34
make                              2             15             17             34
DOS Batch                         1              8              1             26
--------------------------------------------------------------------------------
SUM:                             98           2441           3488          15385
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-09-11T12:54:19Z

Failed to discover a Statement of need section in paper

Kevin-Mattheus-Moerman · 2023-09-11T12:54:40Z

@editorialbot set JOSS_paper as branch

editorialbot · 2023-09-11T12:54:41Z

Done! branch is now JOSS_paper

Kevin-Mattheus-Moerman · 2023-09-11T12:55:46Z

@editorialbot invite @emdupre as editor

editorialbot · 2023-09-11T12:55:51Z

Invitation to edit this submission sent!

emdupre · 2023-09-11T20:43:09Z

Thanks for the invitation, @Kevin-Mattheus-Moerman !

I have a direct COI with one of the coauthors (MN and I were in the same lab until Dec 2022), and I have upcoming publications with several other authors---but no direct involvement---in large consortium papers re: BIDS.

If you think this can be waived, I would need a week to process one of my current submissions that's approaching end of review. But given the recent (< 1 year) shared affiliation with coauthor MN, it might make more sense for me to decline. Let me know what you think, and thanks again !

Kevin-Mattheus-Moerman · 2023-09-12T14:52:26Z

@emdupre thanks for declaring that potential/perceivable COI. I will aim to recruit an alternative editor.

Kevin-Mattheus-Moerman · 2023-09-12T14:52:30Z

@editorialbot invite @britta-wstnr as editor

editorialbot · 2023-09-12T14:52:31Z

Invitation to edit this submission sent!

britta-wstnr · 2023-09-13T06:17:51Z

@Kevin-Mattheus-Moerman I can take this over but only can get started in a week from now since I am travelling for work - if that's okay feel free to assign me!

Kevin-Mattheus-Moerman · 2023-09-13T08:27:27Z

@editorialbot assign @britta-wstnr as editor

editorialbot · 2023-09-13T08:27:30Z

Assigned! @britta-wstnr is now the editor

britta-wstnr · 2023-09-26T14:19:57Z

@CPernet - hi!

First of all, sorry for the delay - I was sick last week.
I am the handling editor for your submission. The first step is to identify reviewers - if you have any ideas for potential reviewers, you can suggest them here --- please read the guidelines in the editorialbot's comment on how to search for reviewers and how to mention them here (do not "@" them, please).

I will be back shortly! 🙂 🌱

CPernet · 2023-09-26T15:17:15Z

No worries - academic life :-)

I have searched but haven't seen someone with the right background in the list -- note that it will be hard to find someone with no COI, apologies in advance.

You could look for 1 reviewer among regular contributors of the whole BIDS project (if that doesn't conflict with journal policy, re coi --> https://github.com/bids-standard/bids-specification/graphs/contributors) as our software builds on that.
for PET expertise - most co-authors from the pre-BIDS consensus paper (2007 - https://journals.sagepub.com/doi/10.1038/sj.jcbfm.9600493#tab-contributors) haven't collaborated in a long time with any of us which should work (authors 1, bob and 15, gitte - to exclude as they are co-author here)

britta-wstnr · 2023-10-06T10:28:58Z

Hi @CPernet ,

Thank you for the suggestions! Just to keep you up to date: I am currently inviting reviewers via email.

britta-wstnr · 2023-10-18T11:04:15Z

@editorialbot check references

editorialbot · 2023-10-18T11:05:33Z

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

OK DOIs

- 10.1038/s41597-022-01164-1 is OK
- 10.1016/j.neuroimage.2015.05.049 is OK
- 10.3389/fninf.2011.00037 is OK
- 10.1385/ni:5:1:11 is OK
- 10.1177/0271678X20905433 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
- 10.5281/zenodo.7795644 is OK

MISSING DOIs

- 10.1038/sdata.2016.44 may be a valid DOI for title: The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments
- 10.3389/fninf.2021.770608 may be a valid DOI for title: BIDScoin: A User-Friendly Application to Convert Source Data to Brain Imaging Data Structure

INVALID DOIs

- None

britta-wstnr · 2023-10-18T11:05:47Z

@editorialbot generate pdf

editorialbot · 2023-10-18T11:07:32Z

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

editorialbot · 2023-10-18T11:08:19Z

Five most similar historical JOSS papers:

PyBIDS: Python tools for BIDS datasets
Submitting author: @tyarkoni
Handling editor: @cMadan (Active)
Reviewers: @grlee77
Similarity score: 0.8671

BIDSonym: a BIDS App for the pseudo-anonymization of neuroimaging datasets
Submitting author: @peerherholz
Handling editor: @oliviaguest (Active)
Reviewers: @deep-introspection, @chrisgorgo, @neuromusic
Similarity score: 0.8495

Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format
Submitting author: @SebastianoF
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @rougier
Similarity score: 0.8294

tacmagic: Positron emission tomography analysis in R
Submitting author: @eebrown
Handling editor: @danielskatz (Active)
Reviewers: @danielskatz
Similarity score: 0.8265

BrainGlobe Atlas API: a common interface for neuroanatomical atlases
Submitting author: @adamltyson
Handling editor: @oliviaguest (Active)
Reviewers: @typically, @vitay
Similarity score: 0.8161

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

britta-wstnr · 2023-10-18T11:18:41Z

Hi @CPernet,
quick update: I am still searching for reviewers.
In the meanwhile, could you please double check the (potentially) missing DOIs and update them (see #5822 (comment))? Thanks! 🙏

CPernet · 2023-10-19T05:20:42Z

thx robot for finding dois :-) added now to the .bib

britta-wstnr · 2023-10-19T09:45:50Z

@editorialbot check references

editorialbot · 2023-10-19T09:46:09Z

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

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.1038/s41597-022-01164-1 is OK
- 10.1016/j.neuroimage.2015.05.049 is OK
- 10.3389/fninf.2011.00037 is OK
- 10.1385/ni:5:1:11 is OK
- 10.1177/0271678X20905433 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
- 10.3389/fninf.2021.770608 is OK
- 10.5281/zenodo.7795644 is OK

MISSING DOIs

- None

INVALID DOIs

- None

britta-wstnr · 2023-10-19T09:47:31Z

Thanks @CPernet, looks good now!

britta-wstnr · 2023-10-25T09:28:40Z

@nbeliy has agreed via email to review - thank you! 🙏
The reviewing process will start as soon as I have found a sufficient number of reviewers. I will ping you then.

CPernet · 2023-10-25T16:57:47Z

@agt24 would you have ideas for reviewers? maybe some PET people at NIH whom we don't work with?

britta-wstnr · 2023-10-27T07:08:39Z

@adswa has agreed via email to review - thank you! 🙏
The reviewing process will start as soon as I have found a sufficient number of reviewers. I will ping you then.

britta-wstnr · 2023-11-20T10:28:53Z

@pjtoussaint has agreed via email to review - thank you! 🙏
With that, we can move this paper into the actual reviewing process. 🌱 That will close this issue and start a new one for the actual review - you will get pinged there and there will be explanations how to proceed.

britta-wstnr · 2023-11-20T10:29:12Z

@editorialbot add @nbeliy as reviewer

editorialbot · 2023-11-20T10:29:15Z

@nbeliy added to the reviewers list!

britta-wstnr · 2023-11-20T10:29:37Z

@editorialbot add @adswa as reviewer

editorialbot · 2023-11-20T10:29:40Z

@adswa added to the reviewers list!

britta-wstnr · 2023-11-20T10:29:55Z

@editorialbot add @pjtoussaint as reviewer

editorialbot · 2023-11-20T10:29:58Z

@pjtoussaint added to the reviewers list!

britta-wstnr · 2023-11-20T10:30:52Z

@editorialbot start review

editorialbot · 2023-11-20T10:30:56Z

OK, I've started the review over in #6067.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 10, 2023

This comment was marked as outdated.

Sign in to view

editorialbot added the TeX label Sep 10, 2023

editorialbot added Makefile Matlab Ruby labels Sep 11, 2023

editorialbot assigned britta-wstnr Sep 13, 2023

editorialbot closed this as completed Nov 20, 2023

[PRE REVIEW]: PET2BIDS: a library for converting Positron Emission Tomography data to BIDS #5822

[PRE REVIEW]: PET2BIDS: a library for converting Positron Emission Tomography data to BIDS #5822

Comments

editorialbot commented Sep 10, 2023 • edited Loading

Status

editorialbot commented Sep 10, 2023

This comment was marked as outdated.

editorialbot commented Sep 10, 2023

editorialbot commented Sep 10, 2023

editorialbot commented Sep 10, 2023

editorialbot commented Sep 10, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

editorialbot commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

editorialbot commented Sep 11, 2023

editorialbot commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

editorialbot commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

editorialbot commented Sep 11, 2023

emdupre commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 12, 2023

Kevin-Mattheus-Moerman commented Sep 12, 2023

editorialbot commented Sep 12, 2023

britta-wstnr commented Sep 13, 2023

Kevin-Mattheus-Moerman commented Sep 13, 2023

editorialbot commented Sep 13, 2023

britta-wstnr commented Sep 26, 2023

CPernet commented Sep 26, 2023

britta-wstnr commented Oct 6, 2023

britta-wstnr commented Oct 18, 2023

editorialbot commented Oct 18, 2023

britta-wstnr commented Oct 18, 2023

editorialbot commented Oct 18, 2023

editorialbot commented Oct 18, 2023

britta-wstnr commented Oct 18, 2023

CPernet commented Oct 19, 2023

britta-wstnr commented Oct 19, 2023

editorialbot commented Oct 19, 2023

britta-wstnr commented Oct 19, 2023

britta-wstnr commented Oct 25, 2023

CPernet commented Oct 25, 2023 • edited Loading

britta-wstnr commented Oct 27, 2023

britta-wstnr commented Nov 20, 2023

britta-wstnr commented Nov 20, 2023

editorialbot commented Nov 20, 2023

britta-wstnr commented Nov 20, 2023

editorialbot commented Nov 20, 2023

britta-wstnr commented Nov 20, 2023

editorialbot commented Nov 20, 2023

britta-wstnr commented Nov 20, 2023

editorialbot commented Nov 20, 2023

editorialbot commented Sep 10, 2023 •

edited

Loading

CPernet commented Oct 25, 2023 •

edited

Loading