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

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whedon opened this issue Mar 14, 2021 · 38 comments
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[PRE REVIEW]: TE-dependent analysis of multi-echo fMRI with *tedana* #3103

whedon opened this issue Mar 14, 2021 · 38 comments

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@whedon
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whedon commented Mar 14, 2021

Submitting author: @tsalo (Taylor Salo)
Repository: https://github.com/ME-ICA/tedana
Version: 0.0.9
Editor: @oliviaguest
Reviewers: @martinagvilas, @stebo85
Managing EiC: Arfon Smith

⚠️ 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.

Author instructions

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

@tsalo 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

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
@whedon
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whedon commented Mar 14, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ 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.

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
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whedon commented Mar 14, 2021

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.48 s (195.0 files/s, 34218.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          50           1593           3538           5052
reStructuredText                19            700            646           1747
Jupyter Notebook                 2              0           1127            571
Markdown                         7            171              0            523
YAML                             7             24             20            342
JSON                             1              0              0            117
Bourne Shell                     2             25             62             64
HTML                             2              5              1             57
make                             2             13              6             34
DOS Batch                        1              8              1             27
CSS                              1              3              3             14
-------------------------------------------------------------------------------
SUM:                            94           2542           5404           8548
-------------------------------------------------------------------------------


Statistical information for the repository '4af636ce7f1bbede560a820c' was
gathered on 2021/03/14.
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
Daniel Handwerker                5           397            115            1.26
Dylan                            2           115              5            0.30
Elizabeth DuPre                 89          8895           4694           33.44
Eneko Uruñuela                   2           860             32            2.20
Frode Aannevik                  14           463            482            2.33
Joshua Teves                    18           503            447            2.34
Logan                           43           256             59            0.78
Logan Dowdle                    13           525            128            1.61
Ross Markello                   28          2575           1645           10.38
Stefano Moia                     2            29             26            0.14
Taylor Salo                    230         10245           7617           43.96
TomMaullin                       1             9             38            0.12
Zaki A                           7            43             42            0.21
monicayao                       11           357             11            0.91

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         16.8                0.00
Cesar Caballero Gaud          8          100.0         12.8               87.50
Chris Markiewicz              7           87.5         16.4               28.57
Dylan                        10            8.7         38.8               20.00
Elizabeth DuPre            3893           43.8         24.7               15.59
Eneko Uruñuela              814           94.7         13.7               10.32
Frode Aannevik              182           39.3         28.3                9.89
Joshua Teves                382           75.9         15.3               12.57
Logan                       127           49.6         19.9               11.02
Ross Markello               205            8.0         33.1               13.17
Stefano Moia                  5           17.2         15.2                0.00
Taylor Salo                4241           41.4         18.9                8.72
TomMaullin                    1           11.1         33.0                0.00
Zaki A                       43          100.0          0.8                0.00
monicayao                   263           73.7         18.0               15.59

@whedon
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whedon commented Mar 14, 2021

PDF failed to compile for issue #3103 with the following error:

Can't find any papers to compile :-(

@tsalo tsalo mentioned this issue Mar 14, 2021
3 tasks
@tsalo
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tsalo commented Mar 14, 2021

The manuscript is located at https://github.com/ME-ICA/tedana/blob/joss/paper/paper.md. Is there a way to make it easier for the bot to locate it?

@emdupre
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emdupre commented Mar 14, 2021

Let's try :

@whedon generate pdf from branch joss

@arfon
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arfon commented Mar 14, 2021

@whedon generate pdf from branch joss

@whedon
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whedon commented Mar 14, 2021

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

@arfon
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arfon commented Mar 14, 2021

@emdupre - thanks. Whedon is a little fussy and expects the command as the first string in a comment...

@whedon
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whedon commented Mar 14, 2021

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

@arfon
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arfon commented Mar 14, 2021

@whedon invite @jni as editor

👋 @jni - would you be able to edit this paper for JOSS?

@whedon
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whedon commented Mar 14, 2021

@jni has been invited to edit this submission.

@arfon
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arfon commented Mar 14, 2021

@whedon invite @cMadan as editor

👋 @cMadan - would you be able to edit this submission for JOSS?

@whedon
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whedon commented Mar 14, 2021

@cMadan has been invited to edit this submission.

@jni
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jni commented Mar 15, 2021

@arfon I only have bandwidth for one more concurrent submission (really -1, but I'll stretch a bit! 😅), so I'll decline this one. 🙏

@tsalo
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tsalo commented Mar 16, 2021

Here are a list of 15 potential reviewers we felt would be well-suited for this manuscript:

  • Athanasiamo
  • JonathanReardon
  • SRSteinkamp
  • TomDonoghue
  • a3sha2
  • arokem
  • grlee77
  • hanayik
  • lukassnoek
  • martinagvilas
  • mwegrzyn
  • puolival
  • sappelhoff
  • sealhuang
  • spinicist

@cMadan
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cMadan commented Mar 16, 2021

I don't think I can take on another review at this time, sorry!

@arfon arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 17, 2021
@arfon
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arfon commented Mar 17, 2021

@tsalo - it looks like the editors best-placed to handle this submission are a little busy right now. I'm going to mark this as 'waitlisted' and we'll assign an editor just as soon as one becomes available. Thanks in advance for your patience!

@danielskatz
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👋 @oliviaguest - Is this a submission you might be able to edit?

@danielskatz
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@whedon invite @oliviaguest as editor

@whedon
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whedon commented May 13, 2021

@oliviaguest has been invited to edit this submission.

@oliviaguest
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I can but not in any immediate way — is it OK to take it on but "pause" it for a few weeks? 😊

@danielskatz
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Yes, that's fine - I'll assign it to you, and when you are ready to start, please remove the 'waitlisted' label and go ahead

@danielskatz
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@whedon assign @oliviaguest as editor

@whedon
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whedon commented May 14, 2021

OK, the editor is @oliviaguest

@tsalo
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tsalo commented Jun 16, 2021

We just want to check in on this and see if there's anything needed from us to move this forward.

@oliviaguest
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@tsalo thank you for checking, short answer: no. Longer answer: I am swamped with work, other duties as editor, etc., but will reach out to reviewers starting (hopefully) next week, Monday. Thus removing the waitlist tag. But I promise you I have neither forgotten, nor absconded my duties more generally here. ☺️

@tsalo
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tsalo commented Jun 17, 2021

Thank you @oliviaguest! We're happy to wait. We're just glad to have a better understanding of the timeline.

@arfon arfon removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jun 19, 2021
@oliviaguest
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@whedon add @martinagvilas as reviewer

@whedon
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whedon commented Jun 21, 2021

OK, @martinagvilas is now a reviewer

@arfon
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arfon commented Aug 8, 2021

👋 @oliviaguest, I wonder if jsheunis, szorowi1, or SRSteinkamp might be able to act as a second reviewer here?

@oliviaguest
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@arfon I'll try them! Thanks!

@oliviaguest
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oliviaguest commented Aug 11, 2021

Ah, @arfon... spoke too soon!

jsheunis unfortunately cannot review this because they are an author on the paper. Made the same mistake months ago when I asked them, ha! In the case of szorowi1, they don't reply to my emails... 😅

@emdupre
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emdupre commented Aug 11, 2021

For additional reviewers, I might also suggest :

robbisg
htwangtw
richford
Remi-Gau
matteomancini
dr-xenia
snastase
kasbohm

@oliviaguest
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@whedon add @stebo85 as reviewer

@whedon
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whedon commented Aug 30, 2021

OK, @stebo85 is now a reviewer

@oliviaguest
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@whedon start review

@whedon
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whedon commented Aug 30, 2021

OK, I've started the review over in #3669.

@whedon whedon closed this as completed Aug 30, 2021
@oliviaguest
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👋 @martinagvilas, @stebo85 please go to #3669 to start the process of reviewing this paper! 😊

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