[PRE REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #6630

editorialbot · 2024-04-16T07:53:52Z

Submitting author: @htwangtw (Hao-Ting Wang)
Repository: https://github.com/bids-apps/giga_connectome
Branch with paper.md (empty if default branch):
Version: 0.5.0
Editor: @mstimberg
Reviewers: @jdkent, @shnizzedy
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9edfa53b0ee4d33931cff3b5429e9c27"><img src="https://joss.theoj.org/papers/9edfa53b0ee4d33931cff3b5429e9c27/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9edfa53b0ee4d33931cff3b5429e9c27/status.svg)](https://joss.theoj.org/papers/9edfa53b0ee4d33931cff3b5429e9c27)

Author instructions

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

@htwangtw 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.

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

editorialbot · 2024-04-16T07:53:54Z

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:

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editorialbot · 2024-04-16T07:54:11Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1873.6 files/s, 124311.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            357            383           1350
Markdown                        10            250              0            689
YAML                            11             41             38            444
TeX                              1             21              0            260
JSON                            16              0              0            178
TOML                             1             13              3            117
INI                              1              3              6             36
reStructuredText                 2             20             29             29
DOS Batch                        1              8              1             26
Jinja Template                   1              7              0             21
Dockerfile                       1              9              1             15
make                             1              4              7              9
SVG                              1              0              1              3
-------------------------------------------------------------------------------
SUM:                            66            733            469           3177
-------------------------------------------------------------------------------

Commit count by author:

    60	Hao-Ting Wang
    55	Remi Gau
     8	dependabot[bot]
     6	htwangtw
     2	pre-commit-ci[bot]
     1	Quentin Dessain

editorialbot · 2024-04-16T07:54:15Z

Paper file info:

📄 Wordcount for paper.md is 1068

✅ The paper includes a Statement of need section

editorialbot · 2024-04-16T07:54:17Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-04-16T07:55:06Z

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

Kevin-Mattheus-Moerman · 2024-04-16T13:31:24Z

@editorialbot check references

editorialbot · 2024-04-16T13:32:13Z

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

OK DOIs

- 10.5281/zenodo.8397156 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1011942 is OK
- 10.1038/s41592-022-01681-2 is OK
- 10.1016/j.schres.2005.11.020 is OK
- 10.1016/j.biopsych.2006.06.027 is OK
- 10.1176/appi.ajp.162.7.1256 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1093/cercor/bhx179 is OK
- 10.12688/mniopenres.12767.2 is OK
- 10.1016/j.neuroimage.2020.117126 is OK
- 10.1002/hbm.25829 is OK
- 10.1101/2021.12.01.470790 is OK
- 10.1089/brain.2012.0073 is OK
- 10.1101/2023.11.20.567926 is OK
- 10.1038/mp.2013.78 is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.3389/fnsys.2012.00062 is OK

MISSING DOIs

- No DOI given, and none found for title: Investigating the convergence of resting-state fun...

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2024-04-16T13:40:55Z

@htwangtw Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. If needed, you can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

Note I've also added the query scope label. This is because I need some help from the editorial board to determine if this work is in scope for JOSS. This mainly relates to the size of this work in terms of number of lines of code. The scope review by the editorial board will check if this conforms to our substantial scholarly effort criteria, and should take about 2 weeks to complete.

htwangtw · 2024-04-16T15:10:51Z

Hi @Kevin-Mattheus-Moerman the flagged paper is a registered report hence there's no doi yet. I can ask the author to see what's possible.

Kevin-Mattheus-Moerman · 2024-04-16T16:01:31Z

Hi @Kevin-Mattheus-Moerman the flagged paper is a registered report hence there's no doi yet. I can ask the author to see what's possible.

@htwangtw that's okay. If it currently has no DOI you can leave it without. Perhaps instead add a URL if you haven't already. Thanks

htwangtw · 2024-04-22T18:16:03Z

@editorialbot generate pdf

editorialbot · 2024-04-22T18:17:19Z

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

htwangtw · 2024-04-22T18:26:49Z

@Kevin-Mattheus-Moerman The added URL will be online by Thursday as OSF requires 48 hours to verify.

htwangtw · 2024-04-23T21:39:49Z

@editorialbot check references

editorialbot · 2024-04-23T21:40:06Z

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

OK DOIs

- 10.5281/zenodo.8397156 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1011942 is OK
- 10.1038/s41592-022-01681-2 is OK
- 10.1016/j.schres.2005.11.020 is OK
- 10.1016/j.biopsych.2006.06.027 is OK
- 10.1176/appi.ajp.162.7.1256 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1093/cercor/bhx179 is OK
- 10.12688/mniopenres.12767.2 is OK
- 10.1016/j.neuroimage.2020.117126 is OK
- 10.1002/hbm.25829 is OK
- 10.1101/2021.12.01.470790 is OK
- 10.1089/brain.2012.0073 is OK
- 10.1101/2023.11.20.567926 is OK
- 10.1038/mp.2013.78 is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.3389/fnsys.2012.00062 is OK

MISSING DOIs

- No DOI given, and none found for title: Investigating the convergence of resting-state fun...

INVALID DOIs

- None

htwangtw · 2024-04-23T21:42:52Z

@editorialbot generate pdf

editorialbot · 2024-04-23T21:44:06Z

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

htwangtw · 2024-04-23T21:45:16Z

@editorialbot check references

editorialbot · 2024-04-23T21:45:32Z

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

OK DOIs

- 10.5281/zenodo.8397156 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1011942 is OK
- 10.1038/s41592-022-01681-2 is OK
- 10.1016/j.schres.2005.11.020 is OK
- 10.1016/j.biopsych.2006.06.027 is OK
- 10.1176/appi.ajp.162.7.1256 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1093/cercor/bhx179 is OK
- 10.12688/mniopenres.12767.2 is OK
- 10.1016/j.neuroimage.2020.117126 is OK
- 10.17605/OSF.IO/T7JKZ is OK
- 10.1002/hbm.25829 is OK
- 10.1101/2021.12.01.470790 is OK
- 10.1089/brain.2012.0073 is OK
- 10.1101/2023.11.20.567926 is OK
- 10.1038/mp.2013.78 is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.3389/fnsys.2012.00062 is OK

MISSING DOIs

- None

INVALID DOIs

- None

htwangtw · 2024-04-26T14:35:50Z

@Kevin-Mattheus-Moerman all that I can do on my side are good. Are we just waiting on the assessment of scope now?

Kevin-Mattheus-Moerman · 2024-04-30T11:35:30Z

@htwangtw yes we were waiting for the scope review. We've just concluded the review and I can share that is was determined this work may be in scope for JOSS. As such I will proceed to find a handing editor.

Kevin-Mattheus-Moerman · 2024-04-30T11:36:46Z

@htwangtw I've just waitlisted this submission since all editors in this domain are currently handling other submissions. We will assign an editor as soon as one becomes available. Thanks for your patience.

Kevin-Mattheus-Moerman · 2024-05-01T20:28:32Z

@editorialbot invite @spholmes as editor

editorialbot · 2024-05-01T20:28:35Z

Invitation to edit this submission sent!

spholmes · 2024-05-03T10:25:57Z

Sorry @Kevin-Mattheus-Moerman I have to decline. I just recieved three requests for reviews in the next few weeks and now traveling, so I have to pass on this one which is quite far from my expertise.

htwangtw · 2024-05-07T20:41:10Z

@Kevin-Mattheus-Moerman We can extend to the Social, Behavioral, and Cognitive Sciences topic for potential editor, if that helps!

Kevin-Mattheus-Moerman · 2024-05-26T13:14:16Z

@htwangtw unfortunately all editors, including the that domain, are busy. I'll assign one as soon as one becomes available. Apologies for the delay so far.

Kevin-Mattheus-Moerman · 2024-05-27T11:35:16Z

@editorialbot invite @Nikoleta-v3 as editor

editorialbot · 2024-05-27T11:35:18Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2024-05-29T12:38:42Z

@Nikoleta-v3 👋

Kevin-Mattheus-Moerman · 2024-05-30T07:30:46Z

@editorialbot invite @mstimberg as editor

editorialbot · 2024-05-30T07:30:49Z

Invitation to edit this submission sent!

mstimberg · 2024-05-30T07:51:43Z

@editorialbot assign me as editor

Happy to edit this submission!

editorialbot · 2024-05-30T07:51:46Z

Assigned! @mstimberg is now the editor

mstimberg · 2024-05-30T08:28:26Z

👋 @htwangtw I will be the editor for your submission, looking forward to working with you again (you were a reviewer for a submission I edited 😊 ).
The first step is to look for reviewers. I will do this mostly over email, so don't be surprised if you won't see much activity here. 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.

htwangtw · 2024-05-30T20:56:32Z

People on BEP17 or BEP12, BEP38 would all be good candidates and I genuinely want their feedback on the output data structures.

I would like peerherholz to review this but I will leave it up to him to see if this is suitable.

mstimberg · 2024-05-31T09:11:39Z

Thanks @htwangtw, this gives me plenty to work with.

PeerHerholz · 2024-05-31T15:02:17Z

Hi folks,

thanks for the offer.

I would love to review this submission but unfortunately, my schedule is rather packed until mid-July and thus,
I won't have to do the work this deserves. However, @htwangtw if you want to chat about output structures and metadata, please let me know. I should definitely have 1-2 h for this.

Thanks and sorry again.

Best, Peer

mstimberg · 2024-06-11T08:58:12Z

@editorialbot add @jdkent as reviewer

Thanks a lot for helping out!

editorialbot · 2024-06-11T08:58:14Z

@jdkent added to the reviewers list!

mstimberg · 2024-06-25T12:48:23Z

Thanks for your patience @htwangtw and @jdkent – I am still trying to find more reviewers. I have contacted a few more potential candidates over email, hopefully I'll hear back from one of them soon.

mstimberg · 2024-07-30T16:04:10Z

@editorialbot add @shnizzedy as reviewer

Many thanks for joining us!

editorialbot · 2024-07-30T16:04:12Z

@shnizzedy added to the reviewers list!

mstimberg · 2024-07-30T16:05:47Z

@htwangtw Apologies again for the long delay in finding reviewers – it doesn't take that long usually… But I am very happy to have @jdkent and @shnizzedy on board, looking forward to a smooth and constructive reviewing process!

mstimberg · 2024-07-30T16:05:57Z

@editorialbot start review

editorialbot · 2024-07-30T16:06:01Z

OK, I've started the review over in #7061.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Apr 16, 2024

editorialbot added Python TeX Jinja labels Apr 16, 2024

Kevin-Mattheus-Moerman added the query-scope Submissions of uncertain scope for JOSS label Apr 16, 2024

Kevin-Mattheus-Moerman removed the query-scope Submissions of uncertain scope for JOSS label Apr 30, 2024

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 30, 2024

editorialbot assigned mstimberg May 30, 2024

mstimberg removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label May 30, 2024

editorialbot closed this as completed Jul 30, 2024

[PRE REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #6630

[PRE REVIEW]: Giga Connectome: a BIDS-app for time series and functional connectome extraction #6630

Comments

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