[PRE REVIEW]: Virtual Scanner: MRI on a Browser

[whedon]

Submitting author: @imr-framework (Sairam Geethanath)
Repository: https://github.com/imr-framework/virtual-scanner
Version: 1.0.0
Editor: @arokem
Reviewers: @nstikov, @vsoch

Author instructions

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

@imr-framework if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

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[whedon]

Hello human, I'm @whedon, 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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This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1590 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1590 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[sairamgeethanath]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[sairamgeethanath]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kyleniemeyer]

Hi @sairamgeethanath, thanks for your submission to JOSS! I'm about to assign an editor to handle your submission, but first:

JOSS only considers software with a clear research application. Your submission looks interesting, but the paper and documentation seem to focus more on educational/training applications. We think your tool does in fact have research applications, but they aren't currently clear. Can you revise your paper to discuss this more?

[kyleniemeyer]

@whedon assign @arokem as editor

[whedon]

OK, the editor is @arokem

[arokem]

👋 @TheChymera : would you be willing to review this paper for JOSS?

[arokem]

@TheChymera : would you be willing to review this submission for JOSS?

[sairamgeethanath]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[TheChymera]

@arokem thank you for your consideration.

As a developer, I am not at all familiar with web applications, and as a user I have always found them unwieldy to integrate into other workflows. It is entirely possible that given this design choice by the authors, my review will be both slower and more critical, than if it were coming from someone who can actually compare the application to what can be expected of web apps in general.

I would encourage you to ask other potential reviewers, including @damaggu . If none other can be found, I could try looking into this no earlier than late August.

[arokem]

Thanks @TheChymera : let's see if I can't find someone to get on this earlier.

[arokem]

@imr-framework : do you have any suggestions from the list of potential reviewers?

[arokem]

👋 @pgadige: would you be willing to review this paper for JOSS? Your expertise in web applications should come in handy.

👋 @vsoch : would you be willing to review this paper for JOSS? Your unique combination of knowledge about web technologies and MRI makes you uniquely qualified.

[vsoch]

I can't say no after that! :)

I'd be happy to, I'm also about to review #1595 so please keep that in mind. I'm not sure that @imr-framework would want me to, however, because I don't see any reproducible containers or tests and these would be required (on top of the normal boxes we check off) to give a thumbs up for publication.

[arokem]

Great. Thanks!

[arokem]

@assign vsoch as reviewer

[arokem]

Let's see if I can't get on more reviewer before kicking off the review

[arokem]

👋 @spinicist : would you be willing to review this paper for JOSS? Your expertise in MRI will be useful here.

[spinicist]

Hello, what's the time frame on this? I will be on leave soon and am unlikely to get to it before I go, so there could be a substantial delay in my input. If that's acceptable I'm very happy to review.

[arokem]

Hi @spinicist : thanks. How substantial is substantial (when do you think that you will be able to get to it)?

[spinicist]

Realistically, early September.

[arokem]

Thanks! Let me see if I can get someone else who would be willing to give this a look earlier than that.

[arokem]

I am having difficulties finding another reviewer for this paper.

@imr-framework : do you have any suggestions for potential reviewers?

[sairamgeethanath]

Here are some names/emails of potential reviewers: 1. Nikola Stikov [email protected] 2. Jonathan Tamir [email protected] 3. Jon-Fredrick Nielsen [email protected] I am more than happy to provide a few more from the open-source Magnetic Resonance Imaging (https://www.opensourceimaging.org/) community if need be.

…

On Fri, Aug 9, 2019 at 9:03 AM Ariel Rokem ***@***.***> wrote: I am having difficulties finding another reviewer for this paper. @imr-framework <https://github.com/imr-framework> : do you have any suggestions for potential reviewers? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1590?email_source=notifications&email_token=AHLQWAJPZTRP6MIPWFDMPXDQDVTJZA5CNFSM4IGB6AOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD36TMNA#issuecomment-519910964>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHLQWAM5KLMDSJXTYAOXFSDQDVTJZANCNFSM4IGB6AOA> .

-- *Sairam Geethanath, Ph.D.* “There are plenty of compelling reasons to push MRI to be more powerful, but that’s one facet of advancing the field. Another is delivering it to the world.”

[arokem]

OK. I contacted @nstikov who has agreed to do the review in tandem with @mathieuboudreau.

I'll add @nstikov to the review and launch the review forum and @mathieuboudreau is welcome to chime in there or on the project issues as well.

[arokem]

@whedon assign @nstikov as reviewer

[whedon]

OK, the reviewer is @nstikov

[arokem]

@whedon add @vsoch as reviewer

[whedon]

OK, @vsoch is now a reviewer

[arokem]

@whedon start review

[whedon]

OK, I've started the review over in #1637. Feel free to close this issue now!

[arokem]

OK - @vsoch, @nstikov and @mathieuboudreau, please head over to #1637 for your review checklists and for the up-to-date pdf of the manuscript. Let me know if you have any questions. Thanks a lot!