[REVIEW]: TE-dependent analysis of multi-echo fMRI with tedana #3669

whedon · 2021-08-30T09:53:53Z

Submitting author: @tsalo (Taylor Salo)
Repository: https://github.com/ME-ICA/tedana
Version: 0.0.9
Editor: @oliviaguest
Reviewer: @martinagvilas, @stebo85
Archive: 10.5281/zenodo.5541689

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Software paper

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✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 (@tsalo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

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

whedon · 2021-08-30T09:53:57Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @martinagvilas, @stebo85 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

whedon · 2021-08-30T09:54:15Z

PDF failed to compile for issue #3669 with the following error:

 Can't find any papers to compile :-(

whedon · 2021-08-30T09:54:18Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.17 s (562.5 files/s, 110948.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          50           1662           3691           5792
reStructuredText                14            852            647           1853
Jupyter Notebook                 2              0           1127            571
Markdown                         7            173              0            533
JSON                             3              0              0            423
YAML                             7             25             20            386
HTML                             3             22              1            212
JavaScript                       1              6              2             82
Bourne Shell                     2             25             62             64
make                             2             14              6             36
DOS Batch                        1              8              1             27
CSS                              1              3              3             14
-------------------------------------------------------------------------------
SUM:                            93           2790           5560           9993
-------------------------------------------------------------------------------


Statistical information for the repository '493aac7d591c96d12e5891a6' was
gathered on 2021/08/30.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Benoît Béranger                  1             3              1            0.01
Cesar Caballero Gaud             1             8              2            0.02
Chris Markiewicz                 2             8              2            0.02
Dan Handwerker                   1             5              5            0.02
Daniel Handwerker                5           397            115            1.09
Dylan                            2           115              5            0.25
Elizabeth DuPre                 90          8897           4696           28.81
Eneko Uruñuela                   3           862             34            1.90
Frode Aannevik                  14           463            482            2.00
Joshua Teves                    21           517            453            2.06
Logan                           43           256             59            0.67
Logan Dowdle                    13           525            128            1.38
Ross Markello                   28          2575           1645            8.94
Stefano Moia                     2            29             26            0.12
Taylor Salo                    249         14018          10347           51.64
TomMaullin                       1             9             38            0.10
Zaki A                           9            46             44            0.19
monicayao                       11           357             11            0.78

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Benoît Béranger               2           66.7         23.0                0.00
Cesar Caballero Gaud          7           87.5         19.1              100.00
Chris Markiewicz              6           75.0         22.6               33.33
Dylan                        10            8.7         45.1               20.00
Elizabeth DuPre            3677           41.3         30.7               15.96
Eneko Uruñuela               28            3.2         19.1                0.00
Frode Aannevik              102           22.0         34.5                7.84
Joshua Teves                365           70.6         20.7               13.42
Logan                       117           45.7         25.9               11.11
Ross Markello               187            7.3         39.4               14.44
Stefano Moia                  3           10.3         21.4                0.00
Taylor Salo                6463           46.1         14.1                7.57
TomMaullin                    1           11.1         39.2                0.00
Zaki A                       27           58.7          6.7                0.00
handwerkerd                   5          100.0          0.9                0.00
monicayao                   235           65.8         24.3               16.17

oliviaguest · 2021-08-30T10:02:18Z

Hi all! 👋 Thank you so much @martinagvilas and @stebo85 for accepting to review this. Please read the instructions above. Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread, so we can all keep track of them. 🌸

For examples of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

whedon · 2021-09-13T09:54:06Z

👋 @stebo85, please update us on how your review is going (this is an automated reminder).

whedon · 2021-09-13T09:54:06Z

👋 @martinagvilas, please update us on how your review is going (this is an automated reminder).

martinagvilas · 2021-09-13T12:21:19Z

@whedon generate pdf from branch joss

whedon · 2021-09-13T12:21:21Z

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon · 2021-09-13T12:21:54Z

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

stebo85 · 2021-09-21T23:18:59Z

The authors addressed one of my comments and deemed the second comment as not feasible. Happy to accept.

oliviaguest · 2021-09-22T12:31:47Z

@martinagvilas are you also happy for this to be accepted? 😊

martinagvilas · 2021-09-24T09:23:44Z

@oliviaguest the authors have addressed my points as well, so happy for this work to be accepted!

oliviaguest · 2021-09-28T12:42:07Z

@tsalo please upload your newest code to a repository like zenodo, etc., and post the DOI here! 😊

oliviaguest · 2021-09-28T12:42:24Z

@whedon generate pdf

whedon · 2021-09-28T12:42:38Z

PDF failed to compile for issue #3669 with the following error:

 Can't find any papers to compile :-(

oliviaguest · 2021-09-28T12:43:09Z

@whedon generate pdf from branch joss

whedon · 2021-09-28T12:43:12Z

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

oliviaguest · 2021-09-28T12:43:30Z

@whedon check references from branch joss

whedon · 2021-09-28T12:43:32Z

Attempting to check references... from custom branch joss

whedon · 2021-09-28T12:43:42Z

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

OK DOIs

- 10.1016/j.neuroimage.2019.116081 is OK
- 10.1073/pnas.1301725110 is OK
- 10.1016/j.neuroimage.2011.12.028 is OK
- 10.1101/2020.12.08.416768 is OK
- 10.1038/s41596-020-0327-3 is OK
- 10.1006/cbmr.1996.0014 is OK
- 10.1016/j.neuroimage.2016.07.049 is OK
- 10.1098/rstb.2002.1114 is OK
- 10.1002/(sici)1522-2594(199907)42:1<87::aid-mrm13>3.0.co;2-o is OK
- 10.1016/j.neuroimage.2020.117461 is OK
- 10.1016/j.celrep.2020.108540 is OK
- 10.1016/j.neuroimage.2009.04.048 is OK
- 10.1016/j.mri.2007.02.014 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1002/mrm.10355 is OK
- 10.1073/pnas.1720985115 is OK
- 10.1016/j.neuroimage.2013.04.001 is OK
- 10.1016/j.neuroimage.2016.12.018 is OK
- 10.1101/2020.10.06.327817 is OK
- 10.1016/j.neuroimage.2005.09.050 is OK
- 10.1109/EMBC44109.2020.9176225 is OK
- 10.1016/j.neuroimage.2021.117914 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-09-28T12:43:44Z

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

tsalo · 2021-09-30T14:14:19Z

@oliviaguest I'm sorry for the delay. We merged the joss branch into main and released 0.0.11. The new DOI is 10.5281/zenodo.5541689.

oliviaguest · 2021-10-11T09:08:12Z

@whedon set 10.5281/zenodo.5541689 as archive

whedon · 2021-10-11T09:08:15Z

OK. 10.5281/zenodo.5541689 is the archive.

oliviaguest · 2021-10-11T09:08:32Z

@whedon recommend-accept

whedon · 2021-10-11T09:08:35Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-11T09:08:49Z

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

OK DOIs

- 10.1016/j.neuroimage.2019.116081 is OK
- 10.1073/pnas.1301725110 is OK
- 10.1016/j.neuroimage.2011.12.028 is OK
- 10.1101/2020.12.08.416768 is OK
- 10.1038/s41596-020-0327-3 is OK
- 10.1006/cbmr.1996.0014 is OK
- 10.1016/j.neuroimage.2016.07.049 is OK
- 10.1098/rstb.2002.1114 is OK
- 10.1002/(sici)1522-2594(199907)42:1<87::aid-mrm13>3.0.co;2-o is OK
- 10.1016/j.neuroimage.2020.117461 is OK
- 10.1016/j.celrep.2020.108540 is OK
- 10.1016/j.neuroimage.2009.04.048 is OK
- 10.1016/j.mri.2007.02.014 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1002/mrm.10355 is OK
- 10.1073/pnas.1720985115 is OK
- 10.1016/j.neuroimage.2013.04.001 is OK
- 10.1016/j.neuroimage.2016.12.018 is OK
- 10.1101/2020.10.06.327817 is OK
- 10.1016/j.neuroimage.2005.09.050 is OK
- 10.1109/EMBC44109.2020.9176225 is OK
- 10.1016/j.neuroimage.2021.117914 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest · 2021-10-11T09:09:00Z

@whedon generate pdf

whedon · 2021-10-11T09:09:14Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2661

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2661, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon · 2021-10-11T09:09:35Z

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

oliviaguest · 2021-10-11T09:09:47Z

@tsalo let us know if the final proofs look good! 😊

tsalo · 2021-10-11T15:00:41Z

The final proof looks good to me. @emdupre does it look good to you too?

emdupre · 2021-10-11T19:46:38Z

Yes, they look good to me !

Thank you, @oliviaguest for editing this submission and @martinagvilas @stebo85 for your thoughtful reviews ! 💛

arfon · 2021-10-12T08:02:57Z

@whedon accept deposit=true

whedon · 2021-10-12T08:03:00Z

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

whedon · 2021-10-12T08:03:44Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-10-12T08:03:45Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03669 joss-papers#2663
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03669
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2021-10-12T09:18:37Z

@martinagvilas, @stebo85 – many thanks for your reviews here and to @oliviaguest for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@tsalo – your paper is now accepted and published in JOSS ⚡🚀💥

whedon · 2021-10-12T09:18:41Z

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03669/status.svg)](https://doi.org/10.21105/joss.03669)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03669">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03669/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03669/status.svg
   :target: https://doi.org/10.21105/joss.03669

This is how it will look in your documentation:

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whedon added Makefile Python review Shell labels Aug 30, 2021

whedon assigned oliviaguest Aug 30, 2021

whedon mentioned this issue Aug 30, 2021

[PRE REVIEW]: TE-dependent analysis of multi-echo fMRI with *tedana* #3103

Closed

tsalo mentioned this issue Aug 30, 2021

JOSS manuscript ME-ICA/tedana#669

Closed

3 tasks

whedon assigned martinagvilas and stebo85 Aug 31, 2021

This was referenced Sep 14, 2021

[JOSS review] Documentation suggestions ME-ICA/tedana#798

Closed

[JOSS review] Manuscript suggestions ME-ICA/tedana#799

Closed

stebo85 mentioned this issue Sep 20, 2021

[JOSS review] Documentation suggestions ME-ICA/tedana#804

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 11, 2021

whedon added accepted published Papers published in JOSS labels Oct 12, 2021

arfon closed this as completed Oct 12, 2021

editorialbot mentioned this issue Dec 20, 2023

[PRE REVIEW]: elsa: an elegant framework for tomographic reconstruction #6164

Closed

[REVIEW]: TE-dependent analysis of multi-echo fMRI with *tedana* #3669

[REVIEW]: TE-dependent analysis of multi-echo fMRI with *tedana* #3669

Comments

whedon commented Aug 30, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @martinagvilas

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @stebo85

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Aug 30, 2021

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tsalo commented Oct 11, 2021

emdupre commented Oct 11, 2021

arfon commented Oct 12, 2021

whedon commented Oct 12, 2021

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arfon commented Oct 12, 2021

whedon commented Oct 12, 2021

[REVIEW]: TE-dependent analysis of multi-echo fMRI with tedana #3669

[REVIEW]: TE-dependent analysis of multi-echo fMRI with tedana #3669

whedon commented Aug 30, 2021 •

edited

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