[REVIEW]: Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@sebastientourbier@osorensen<!--end-editor-- Reviewers: @adbartni, @jsheunis Archive: 10.5281/zenodo.6645256

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/fa1f416a4a6c23fe19bda6f36f123c1e/status.svg)](https://joss.theoj.org/papers/fa1f416a4a6c23fe19bda6f36f123c1e)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@adbartni & @jsheunis, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @jsheunis

📝 Checklist for @adbartni

editorialbot commented 2 years ago

Hello humans, 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:

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=1.34 s (126.1 files/s, 93677.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              3              0             25          65623
Python                          95           6525           9108          25397
reStructuredText                18           1331            409           2152
XML                              2              0              0           1854
YAML                             9             77            115           1720
Jupyter Notebook                 7              0           5607           1196
INI                             10             54              0            917
CSS                              1              0              9            723
TeX                              1             60              0            668
Markdown                         3             81              0            493
HTML                             3             50              2            314
JSON                             6              0              0            228
Dockerfile                       1             43            111            192
DOS Batch                        1             23              1            166
make                             1             24              6            123
Bourne Shell                     7             15             40             66
JavaScript                       1              0              1              1
-------------------------------------------------------------------------------
SUM:                           169           8283          15434         101833
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 2739

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- doi10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

jsheunis commented 2 years ago

Review checklist for @jsheunis

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/connectomicslab/connectomemapper3?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@sebastientourbier) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

jsheunis commented 2 years ago

@osorensen @sebastientourbier

Review update: I've checked most of the boxes in my checklist. The ones that are still open are dependent on open issues, particularly:

sebastientourbier commented 2 years ago

Dear @jsheunis,

Thank you a lot for the time you spent reviewing CMP3 and its paper! I am going to address your issues next week and I will reply directly inside them for the sake of clarity. I will let you all know as soon as it is done.

Best regards

adbartni commented 2 years ago

Review checklist for @adbartni

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/connectomicslab/connectomemapper3?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@sebastientourbier) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 2 years ago

@sebastientourbier can you please update us on how it is going addressing the points raised by the reviewers?

sebastientourbier commented 2 years ago

Dear @osorensen,

Most of all the points have been addressed by separate PRs and a new release incorporated all changes is in preparation.

The PR related to this release can give a list of all the tackled changes:

https://github.com/connectomicslab/connectomemapper3/pull/184

The new paper with the high-level summary is now waiting for approval (https://github.com/connectomicslab/connectomemapper3/pull/175), which will close the issue:

https://github.com/connectomicslab/connectomemapper3/issues/161

Once done, I will update any mention of the version in the paper, and will make the new release.

sebastientourbier commented 2 years ago

Dear all,

I would like to let you know that the release of a new version (3.0.4) that includes all changes is now available.

The new paper is now up-to-date with the new high-level summary on the master branch.

You can consult a summary of the changes at the following URL: https://github.com/connectomicslab/connectomemapper3/releases/tag/v3.0.4

Let me know if I need to do something else.

Best regards

osorensen commented 2 years ago

@editorialbot generate pdf

osorensen commented 2 years ago

Thanks @sebastientourbier. When you have time, could you please check if this is sufficient to complete your review checklist, @adbartni?

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:

osorensen commented 2 years ago

@sebastientourbier, I will now read through the paper once more, and let you know if I have any further comments.

In the meantime, could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

sebastientourbier commented 2 years ago

Thank you @osorensen! I am taking of this.

sebastientourbier commented 2 years ago

@osorensen Here is the information you need related to the latest release:

Tag release: v3.0.4
DOI of the Zenodo record: 10.5281/zenodo.6645256

I also changed the title of the record to match exactly the title of the paper, and checked the list of authors/orcid, and they are the same.

Let me know if you need anything else.

osorensen commented 2 years ago

@editorialbot help

editorialbot commented 2 years ago

Hello @osorensen, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author or reviewer to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# 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 version
@editorialbot set v1.0.0 as version

# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

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@editorialbot query scope

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

# Open the review issue
@editorialbot start review

osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.6645256 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6645256

osorensen commented 2 years ago

@editorialbot set v3.0.4 as version

editorialbot commented 2 years ago

Done! version is now v3.0.4

osorensen commented 2 years ago

@editorialbot check references

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- doi:10.18112/openneuro.ds003505.v1.1.1 is INVALID (failed connection)

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:

osorensen commented 2 years ago

@editorialbot check references

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

osorensen commented 2 years ago

@sebastientourbier can you please try to remove the isbn field from paper.bib. It seems like two papers have such a field, which might cause the issue above. Please let me know when it's done.

osorensen commented 2 years ago

Here are the lines: https://github.com/connectomicslab/connectomemapper3/search?q=isbn&type=

sebastientourbier commented 2 years ago

@osorensen All isbn fields have been removed 👍

osorensen commented 2 years ago

@editorialbot check references

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.3475969 is OK
- 10.1016/J.NEUROIMAGE.2011.08.056 is OK
- 10.1038/nn.4500 is OK
- 10.5281/zenodo.3571874 is OK
- 10.3389/fninf.2019.00001 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/nn.4502 is OK
- 10.1371/journal.pone.0048121 is OK
- 10.3389/conf.fninf.2013.09.00042 is OK
- 10.1016/j.neuroimage.2015.04.042 is OK
- 10.1101/188706 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1016/j.neuroimage.2015.02.065 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1146/annurev-biodatasci-072018-021237 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1162/netn_e_00052 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.5075/epfl-thesis-3230 is OK
- 10.1016/J.NEUROIMAGE.2011.09.015 is OK
- 10.1016/j.clinph.2020.09.018 is OK
- 10.1038/sdata.2018.270 is OK
- 10.1016/j.jneumeth.2011.09.031 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.1038/s41592-021-01185-5 is OK
- 10.5281/ZENODO.3712762 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.21105/joss.01294 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.0010042 is OK
- 10.1016/j.clinph.2019.09.006 is OK
- 10.1038/nn.4550 is OK
- 10.1016/j.nicl.2020.102336 is OK
- 10.1016/j.neuroimage.2020.117137 is OK
- 10.1162/netn_a_00147 is OK
- 10.1002/hbm.25365 is OK
- 10.1016/j.neuroimage.2021.118611 is OK
- 10.1162/netn_a_00218 is OK
- 10.18112/openneuro.ds003505.v1.1.1 is OK
- 10.1038/s41597-021-01116-1 is OK
- 10.1016/j.clinph.2021.10.008 is OK
- 10.1016/j.neuroimage.2009.10.003 is OK
- 10.12688/f1000research.20887.3 is OK
- 10.1101/gr.1239303 is OK
- 10.1101/2022.01.31.478189 is OK
- 10.1162/netn_a_00114 is OK
- 10.1073/PNAS.1922248117 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3299

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3299, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 2 years ago

@sebastientourbier

I checked the archive meta-data and all looks good. :+1:
I checked the version tag for the review and archive and verified they match :+1:
I proofread the paper and have the following comment:
[x] Introduce Magnetic Resonance Imaging (MRI) in the summary where MRI is first used.

sebastientourbier commented 2 years ago

Dear @Kevin-Mattheus-Moerman,

Thank you very much.

I just took care to introduce MRI the very first time it is used in the paper. I also took care of defining BIDS in the summary too. Finally, I noticed that I was redefining CMP3 acronym multiple times and this has been fixed. The changes can be viewed in https://github.com/connectomicslab/connectomemapper3/pull/196.

Let me know if you need anything else. Best

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot generate pdf

openjournals / joss-reviews