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miykael / atlasreader

Python interface for generating coordinate tables and region labels from statistical MRI images
BSD 3-Clause "New" or "Revised" License
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Initiates paper for Journal of Open Source Software (JOSS) #66

Closed miykael closed 5 years ago

miykael commented 6 years ago

Closes https://github.com/miykael/atlasreader/issues/25.

I recently reviewed a paper for the Journal of Open Source Software. The process is very nice and I think JOSS would be a perfect journal for publishing atlasreader. I therefore went already ahead and created the required paper.md and paper.bib files (see this PR).

The bibliography already includes the required python software, and the missing references for the atlases will be added at a later timepoint.

@rmarkello, @danjgale, @PeerHerholz, @KirstieJane, please verify if your affiliation and personal information under paper.md are correct. The order of authors is established through number of commits but can of course be further discussed.

The 250-1000 words summary of the software still needs to be written. I'm happy to do this at a later stage, but of course, I will also not get angry if anyone else wants to do this :-)

codecov-io commented 6 years ago

Codecov Report

Merging #66 into master will not change coverage. The diff coverage is n/a.

Impacted file tree graph

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  Coverage      88%   88%           
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  Files           6     6           
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  Hits          352   352           
  Misses         48    48
Impacted Files Coverage Δ
atlasreader/atlasreader.py 96.03% <ø> (ø) :arrow_up:

Continue to review full report at Codecov.

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miykael commented 5 years ago

Hey @rmarkello, @danjgale, @PeerHerholz and @KirstieJane,

I think I've finalized everything. All PRs and relevant issues are closed. We're only a few steps away from submitting atlasreader to JOSS. If this is still alright with everybody?

  1. I wrote the first draft of the paper today and would appreciate your input and feedback. Feel free to either directly change things or tell me what needs what where. As a reminder, the whole paper should have between 250-1000 words. For more, see the Authors Guidlines.

  2. The current title of the paper is "AtlasReader: A Python package to generate coordinate tables, region labels and informative figures from statistical MRI images". What do you think? Any suggestions for changes?

  3. I've also updated the Readme and the example notebook. So please tell me if you're happy with the changes and if you're ok with me merging this PR.

  4. @danjgale, do you already have an ORCID number? If yes, please add it here.

Thanks again each and everyone for the energy and effort you put into this project. I'm very happy with the end product and can't wait to submit it to JOSS!!!

PeerHerholz commented 5 years ago

Hey @miykael and all,

even though I'll need to spend a closer look tomorrow, at a first glimpse everything looks super cool! I'll provide more detailed and (hopefully) helpful feedback later.

miykael commented 5 years ago

Commit https://github.com/miykael/atlasreader/pull/66/commits/c6a3bd30981a1531a554349dba3f593ac5da6362 incorparated what @KirstieJane was saying in https://github.com/miykael/atlasreader/issues/91. The commit does not contain any content changes, just more new lines, to make reading and version control easier.

PeerHerholz commented 5 years ago

@miykael, @rmarkello, @danjgale: shouldn't we include DOIs, etc. for the packages atlas reader uses in the references?

rmarkello commented 5 years ago

That would probably be good to have in the .bib file, yes! Looks like the DOI is already there for matplotlib—adding it for the others should be relatively quick.

miykael commented 5 years ago

Just pushed the newest suggestion for author name order (suggested by Ross), via https://github.com/miykael/atlasreader/pull/66/commits/9af8dca97642d0cf7354c609114ca42845edefbb.

The order and title of the paper would be: Notter M. P., Gale D., Herholz P., Markello R. D., Notter-Bielser M.-L., & Whitaker K. (2019). AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images. The Journal of Open Source Software, ZZZ, YYY.

What do you guys think?

miykael commented 5 years ago

About the DOIs, yes. That sounds good @PeerHerholz. I went ahead and added the missing ones with https://github.com/miykael/atlasreader/pull/66/commits/849f9fc03b7fba5aeebea8ef886be3f37d089362.

I wasn't able to find the DOI for Scipy or Scikit-learn. Perhaps somebody else has more success?

miykael commented 5 years ago

This PR seems to be finished for now. I will merge this, so that we can create a new release and establish a zenodo reference for this toolbox (as mentioned in https://github.com/miykael/atlasreader/pull/66#discussion_r251507818).

The discussion about the publication should be continued in https://github.com/miykael/atlasreader/issues/25.