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ME-ICA / tedana

TE-dependent analysis of multi-echo fMRI
https://tedana.readthedocs.io
GNU Lesser General Public License v2.1
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JOSS manuscript #669

Closed tsalo closed 2 years ago

tsalo commented 3 years ago

Please see openjournals/joss-reviews#3669

Summary

@emdupre and I have been working on a manuscript for JOSS, and we think it's almost ready for the dev team to review.

Additional Detail

One pending question is how we want to handle the authorship order. @emdupre and I were hoping to be co-first authors, and we discussed having Dan as the last author, but we weren't sure what the order should be from there. I think two good options are (1) alphabetical or (2) sorted by commits/PRs, then alphabetical for non-code contributors.

  1. DuPre, Salo, Caballero-Gaudes, Dowdle, Heunis, Kundu, Markello, Markiewicz, Maullin-Sapey, Moia, Staden, Teves, Uruñuela, Vaziri-Pashkam, Whitaker, & Handwerker
  2. DuPre, Salo, Dowdle, Teves, Markello, Whitaker, Heunis, Uruñuela, Moia, Markiewicz, Caballero-Gaudes, Maullin-Sapey, Kundu, Staden, Vaziri-Pashkam, & Handwerker

    Next Steps

  3. Determine authorship order.
  4. Finish manuscript.
  5. Coauthor review.
  6. Push manuscript to repo.
  7. Submit to JOSS.

EDIT: Just so everyone knows, the author list above is derived from our Zenodo file. For the folks who are on the OHBM abstract, but who aren't in our Zenodo file, I would ask you to respond here saying if you want to be included or not. We would love to include you! The folks who are missing from the Zenodo file are @62442katieb, @angielaird, @notZaki, and Peter Bandettini. I don't think Dr. Bandettini is on GitHub, so it would be great if someone who works with him (@jbteves or @handwerkerd?) could follow up about this. EDIT 2: Here is the link to the draft. I have set the permissions so that anyone with the link can comment, but most folks should have edit access already. If you don't have edit access, and would like it, please email or message me and I'll add you.

Manuscript to-do list:

eurunuela commented 3 years ago

Thank you for the work you're putting into this!

I'm happy with any of the two ordering possibilities and looking forward to reading the manuscript.

jbteves commented 3 years ago

Thanks @tsalo and @emdupre ! @handwerkerd has emailed Peter, so we'll keep you posted on that front. I would opt for alphabetical. I don't think that either will really be a reflection of work put in (number of PRs != total productive output IMO), and alphabetical will be a little more clear for outsiders who the primary and supervisory authors are.

CesarCaballeroGaudes commented 3 years ago

Thank you for this work!! I am also happy with any of the proposed ordering.

handwerkerd commented 3 years ago

If others are ok with it, I'm happy to be senior author and fine with either option for middle authors.

I was initially slightly leaning towards sorting by commits, as a very flawed, but clearly applicable metric of contribution amount. That said, it's really just a snapshot of contributions on the day the manuscript is submitted, so it feels not particularly clear either. I'll leave it to the middle authors - particularly the 3 who are highest by commits after Elizabeth & Taylor: ( @jbteves @dowdlelt @rmarkello ) to voice a preference.

rmarkello commented 3 years ago

Hey all :wave: ! Thanks for doing all this—excited to see tedana turned into a JOSS paper! 🙌

In response to @handwerkerd's query: I'm personally in favor of purely alphabetical, as I don't love the distinction between "code" / "non-code" contributions. In my mind one of the primary goals of tedana was / is to foster a community around multi-echo imaging (tools, resources, data, etc.), and differentiating contributions to that community based on perceived technical merit seems mildly antithetical to that goal. That said, since I'm not very involved in tedana anymore, I'm happy to defer to those who are more active community members if they have a strong preference.

dowdlelt commented 3 years ago

Either way is fine, I have no issues with alphabetical. Thanks so much for the work on it folks - I'm happy to read over, revise, and such - however I can help.

tsalo commented 3 years ago

Thanks to everyone for responding. It looks like most folks are fine with either approach, but there's a slight preference for alphabetical. I'll move forward with that, and if anyone has strong objections we can revisit.

I have offline confirmations from @angielaird, @62442katieb, and Peter Bandettini to include them as coauthors, so I will open a pull request to add them to the Zenodo file.

notZaki commented 3 years ago

Thanks for putting the draft together. Either author order works for me. I am just happy to included.

tsalo commented 3 years ago

@emdupre and I were thinking of requesting feedback by the end of the month, after which I can convert to markdown and open a PR to the repository. I will add the deadline to the tedana calendar. Does anyone have an issue with this deadline?

tsalo commented 3 years ago

Addressed by #693. I will submit in about an hour. Closing this now.

tsalo commented 3 years ago

I realized we should probably keep an issue open to discuss the review process within the project, so I'm reopening this. Also, the pre-review has begun with https://github.com/openjournals/joss-reviews/issues/3103.

tsalo commented 3 years ago

Does anyone have thoughts on reviewers? Most of the folks I'd ask to review a multi-echo software manuscript are on this one, but I'm sure there are some folks out there who I'm missing.

emdupre commented 3 years ago

Does anyone have thoughts on reviewers? Most of the folks I'd ask to review a multi-echo software manuscript are on this one, but I'm sure there are some folks out there who I'm missing.

I don't think they have to be multi-echo experts in particular, but someone who has significant MRI / python packaging experience would be a great fit. You can check who's agreed to review for JOSS already here, and then we'll want to filter by Python and neuroscience expertise !

tsalo commented 3 years ago

I did see that somewhat overwhelming list of ~1700 people... Here are the results of an initial search for folks who mention neuroimaging/MRI in their "topic areas" and Python in their preferred or "other" languages: SRSteinkamp, richford, Athanasiamo, a3sha2, peerherholz, lukassnoek, matteomancini, dr-xenia, puolival, mwegrzyn, mih, grlee77, spinicist, sealhuang

emdupre commented 3 years ago

Some initial ideas from the spreadsheet :

EDIT : jinx :laughing:

KirstieJane commented 3 years ago

There are some great names on those (very similar 😉) lists. Endorse from me ✔️

(Stefan might be a conflict of interest from a BIDS perspective but he may not be and that's for him to say no to not us!)

tsalo commented 3 years ago

Merged list:

handwerkerd commented 3 years ago

I don't know many of the names listed above. Of those, I'm familiar with TomDonoghue & snastase. Additional names: arokem (I'm familiar with him) hanayik (Don't know, but seems like relevant skills)

62442katieb commented 3 years ago

Of that list, there are a few individuals that might have a conflict of interest (dr-xenia, matteomancini, snastase, peerherholz, anibalsolon) as we currently have coauthored publication(s) in prep/under review (the Brainhack NeuroView paper and/or the OSSIG Inclusivity in Virtual Conferences paper) neither of which are published yet. I don't know how if that counts, per JOSS's COI policy, but as @KirstieJane mentioned above it might also be up to them to decide.

tsalo commented 3 years ago

Good thinking @62442katieb! Can everyone try to flag anyone with a possible COI as soon as possible? It would be great to have a list by EOD.

handwerkerd commented 3 years ago

Oy. COIs for high authorship papers in open science are fun. No additional conflicts of interest for me. I am a co-author on the OSSIG Inclusivity in Virtual Conferences paper and a consortium author on the Brainhack NeuroView paper. For both of those manuscripts, i don't think I directly interacted with anyone on the list. If I were a potential JOSS reviewer, I wouldn't recuse myself from peer reviewing any of their manuscripts due to COI guidelines.

emdupre commented 3 years ago

mih would be a COI for me since we co-authored a paper together in the last 4 years; peerherholz and I are in the same lab so also a definite COI.

The bigger OS papers / initiatives I'm leaning towards letting the reviewers themselves decide if they count as a COI (or not). But that's not a strong sense -- I guess it will depend on how many reviewers we can retain after this pass ! :smile:

tsalo commented 3 years ago

How about arokem, martinagvilas, TomDonoghue, and Athanasiamo?

jsheunis commented 3 years ago

Another option could be marcelzwiers (not on the list of existing JOSS reviewers)

handwerkerd commented 3 years ago

martinagvilas' profile says she's a core contributor and maintainer of The Turing Way. Is there a COI with @KirstieJane

The short list is fine with me.

tsalo commented 3 years ago

@emdupre and I talked a bit about this offline, and she brought up the great idea to provide a longer list to the editor. Specifically, we can eliminate anyone from that summary list with a clear COI, and anyone who has a more ambiguous one can recuse themselves in they feel it's necessary. Here's that list of 15 potential reviewers:

tsalo commented 3 years ago

A small update- we are now under active review and have a new JOSS issue: openjournals/joss-reviews#3669.

tsalo commented 3 years ago

@ME-ICA/tedana-devs the JOSS editor has requested that we make a new release to generate a new Zenodo DOI. I think we talked about making a release after our meeting earlier this month, but we just haven't gotten around to it yet. Does anyone have an issue with me releasing 0.0.11 today?

emdupre commented 3 years ago

Are we merging in the JOSS branch before cutting the release, or should we cut a release from the JOSS branch itself ?

jbteves commented 3 years ago

I think we should merge in the JOSS branch.

tsalo commented 3 years ago

+1 to merging in the JOSS branch.

tsalo commented 3 years ago

I put together some release notes. If anyone has time to take a look, that would be great: https://github.com/ME-ICA/tedana/releases/tag/untagged-6eb42636f944dd6e9578

If there anything we need to do before merging in the JOSS branch?

tsalo commented 3 years ago

I just want to check before we move forward with the next release. Does anyone want me to wait for them to review the release notes? Otherwise, I'd like to release by the end of today (~5pm EST).

dowdlelt commented 3 years ago

@tsalo that link gives me a 404

jbteves commented 3 years ago

It also 404s for me, and is not visible in "release notes;" last I see is from May.

tsalo commented 3 years ago

Whoops! I just edited the release-drafter draft, so the May draft (0.0.11) is the one to look at.

dowdlelt commented 3 years ago

I don't see any issues, and the language seems clear. I've been a bit disconnected from the code for a bit, so maybe can't provide the most useful feedback...but I do think it looks good.

eurunuela commented 3 years ago

Looks good to me @tsalo !

tsalo commented 3 years ago

Okay, releasing now.

handwerkerd commented 3 years ago

I didn't comment earlier, but the release notes look great. It's impressive to see how much has changed since the last release, particularly knowing many were substantial changes!

tsalo commented 3 years ago

It's been accepted! Now we just need a PR to add badges to our README and docs/index.rst. The code is available in https://github.com/openjournals/joss-reviews/issues/3669#issuecomment-940826017.