Closed whedon closed 3 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
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Failed to discover a Statement of need
section in paper
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=1.03 s (195.2 files/s, 20620.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 91 2047 3226 8415
Markdown 38 934 0 2644
YAML 35 33 37 833
Jupyter Notebook 1 0 839 808
SVG 6 0 0 367
reStructuredText 25 227 245 259
TeX 1 26 0 222
DOS Batch 1 8 1 26
TOML 1 0 0 16
make 1 4 7 9
INI 1 0 0 4
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SUM: 201 3279 4355 13603
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Statistical information for the repository '2633' was gathered on 2020/09/02.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Adria 30 2514 1582 5.80
MathPlusCode 2 2 6 0.01
Nina Montana Brown 39 2257 639 4.10
Qianye Yang 15 434 83 0.73
RemiDelaunay 40 1982 501 3.52
Shaheer U Saeed 121 5066 1793 9.72
Yipeng Hu 54 1997 1302 4.67
Yunguan Fu 375 27021 20856 67.82
Zachary Baum 15 732 297 1.46
ZheMin 14 158 62 0.31
agrimw 8 747 92 1.19
agrimwood 1 2 2 0.01
ebonmati 22 375 90 0.66
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
Adria 926 36.8 1.1 12.85
MathPlusCode 1 50.0 1.5 0.00
Nina Montana Brown 1198 53.1 1.9 16.36
Qianye Yang 100 23.0 1.2 14.00
RemiDelaunay 770 38.8 1.3 10.39
Shaheer U Saeed 1327 26.2 1.5 20.65
Yipeng Hu 858 43.0 0.8 8.86
Yunguan Fu 7689 28.5 1.8 12.16
Zachary Baum 494 67.5 1.7 11.13
ZheMin 73 46.2 1.4 10.96
agrimw 237 31.7 1.2 13.50
ebonmati 64 17.1 0.7 10.94
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5281/zenodo.3835682 is OK
- 10.5281/zenodo.3715652 is OK
MISSING DOIs
- 10.1109/isbi.2018.8363756 may be a valid DOI for title: Label-driven weakly-supervised learning for multimodal deformable image registration
- 10.1016/j.media.2018.11.010 may be a valid DOI for title: A deep learning framework for unsupervised affine and deformable image registration
- 10.1109/tmi.2019.2897538 may be a valid DOI for title: VoxelMorph: a learning framework for deformable medical image registration
- 10.1016/j.media.2019.07.006 may be a valid DOI for title: Unsupervised learning of probabilistic diffeomorphic registration for images and surfaces
- 10.1016/j.cmpb.2018.01.025 may be a valid DOI for title: NiftyNet: a deep-learning platform for medical imaging
- 10.1109/cvpr.2016.90 may be a valid DOI for title: Deep residual learning for image recognition
- 10.1016/j.neuroimage.2007.07.007 may be a valid DOI for title: A fast diffeomorphic image registration algorithm
- 10.1016/j.neuroimage.2008.10.040 may be a valid DOI for title: Diffeomorphic demons: Efficient non-parametric image registration
- 10.1007/978-3-658-29267-6_53 may be a valid DOI for title: Deep Groupwise Registration of MRI Using Deforming Autoencoders
- 10.1109/42.796284 may be a valid DOI for title: Nonrigid registration using free-form deformations: application to breast MR images
- 10.1002/mp.12268 may be a valid DOI for title: REtroSpective Evaluation of Cerebral Tumors (RESECT): A clinical database of pre-operative MRI and intra-operative ultrasound in low-grade glioma surgeries
INVALID DOIs
- None
Hi @mathpluscode! Thanks for your submission. There are a few things to take care of before proceeding with the review:
@arokem Do you have bandwidth for handling a JOSS submission right now? We have you marked as "somewhat able" but I seem to remember maybe that is overstating it.
@whedon invite @arokem as editor
@arokem has been invited to edit this submission.
Hi @kthyng, thanks for the advice! We will fix this now ;)
Hi @kthyng,
For the reference, does every reference have to have a DOI? Is it ok if some references do not have DOI?
EDIT:
@whedon generate pdf
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK
MISSING DOIs
- 10.1016/j.media.2019.07.006 may be a valid DOI for title: Unsupervised learning of probabilistic diffeomorphic registration for images and surfaces
- 10.1016/j.neuroimage.2007.07.007 may be a valid DOI for title: A fast diffeomorphic image registration algorithm
INVALID DOIs
- None
@kthyng We are fixing these two DOIs now.
For the reference, does every reference have to have a DOI? Is it ok if some references do not have DOI?
Any reference that has a doi needs to include it in your references. It looks like there are two more missing to consider above. If they are correct, they need to be included.
- We've also changed the title from "DeepReg: a deep-learning toolkit for medical image registration" to "DeepReg: a deep learning toolkit for medical image registration", remove the hyphen between deep and learning. Hope it's fine.
I have updated this.
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.media.2019.07.006 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2007.07.007 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon generate pdf
For the reference, does every reference have to have a DOI? Is it ok if some references do not have DOI?
Any reference that has a doi needs to include it in your references. It looks like there are two more missing to consider above. If they are correct, they need to be included.
- We've also changed the title from "DeepReg: a deep-learning toolkit for medical image registration" to "DeepReg: a deep learning toolkit for medical image registration", remove the hyphen between deep and learning. Hope it's fine.
I have updated this.
Hi, @kthyng, we've fixed the DOIs.
Hi @kthyng : thanks for tagging me in here. This looks very interesting, BUT: Yes: things are a bit hectic right now... I would like to be assigned at most one paper at a time, for the near future. As I am already assigned to #2589, which is just getting started, I would really appreciate if you could find someone else to shepherd this submission. Sorry!
@arokem Totally understand! No worries!
Hey @Kevin-Mattheus-Moerman! Could you edit this submission?
@whedon invite @Kevin-Mattheus-Moerman as editor
@Kevin-Mattheus-Moerman has been invited to edit this submission.
@whedon assign me as editor
OK, the editor is @Kevin-Mattheus-Moerman
Hi @kthyng @Kevin-Mattheus-Moerman,
Is there anything we need to do from author part? Or we just need to be patient and wait for the submission to be under review?
Thx!
@mathpluscode at this point I'm looking for reviewers for this submission and will invite some shortly. If you have any suitable reviewers in mind please suggest them here (remove the @ when you quote GitHub handles).
@mathpluscode at this point I'm looking for reviewers for this submission and will invite some shortly. If you have any suitable reviewers in mind please suggest them here (remove the @ when you quote GitHub handles).
@Kevin-Mattheus-Moerman I checked the reviewer lists and maybe we'd like to suggest ethanwharris, mamrehn, billchenxi.
@mathpluscode thanks. I'll check those out. FYI they needn't be just from that list, I can also invite new reviewers
@mathpluscode thanks. I'll check those out. FYI they needn't be just from that list, I can also invite new reviewers
@Kevin-Mattheus-Moerman sure! We will ask around and recommend more if people are available. Thanks!
@stefanklein @mstaring @thewtex @ljod @fedorov @ethanwharris @mamrehn @billchenxi as editor for the Journal of Open Source Software (JOSS) I'd like to invite you to review "DeepReg: a deep learning toolkit for medical image registration".
You can comment here to let me know if you are interested. Thanks!
We have a smooth GitHub based review process which focuses on the software :computer: as well as the very short paper :page_facing_up: .
This here is a "pre-review issue". Once I've attracted sufficient reviewers I'll initiate a review issue where reviewers have a set of check-boxes to guide them through the review process.
Check out our documentation to learn more about what it is like to review for JOSS, also here is an example review process for a different submission which you can look at: https://github.com/openjournals/joss-reviews/issues/2520
Thanks!
Hi @Kevin-Mattheus-Moerman, I'd be happy to review this :smiley:
@whedon assign @ethanwharris as reviewer
OK, @ethanwharris is now a reviewer
I am less into the code with this, but perhaps @hsokooti may be interested.
Hi, thanks for the invitation to review. I hadn't heard about this journal. The concept seems very interesting! Unfortunately I won't have time to do this review and thoroughly test the code. A postdoc from my group with experience in image registration and deep learning would be interested in doing the review, so please consider inviting her: @lbrea . Best regards, Stefan
Thanks @stefanklein, that is fine. @lbrea would you be able to review this work? Let me know and I can add you, thanks!
Yes, please feel free to add me for the review
Best,
Luisa
On Fri, Sep 18, 2020 at 5:09 PM Kevin Mattheus Moerman < notifications@github.com> wrote:
Thanks @stefanklein https://github.com/stefanklein, that is fine. @lbrea https://github.com/lbrea would you be able to review this work? Let me know and I can add you, thanks!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2633#issuecomment-694924007, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMAQ7BXTAGX6YJBMVFQI33DSGNZZBANCNFSM4QTVCY7Q .
Sorry for the delay in responding. I don't think I will be able to make time to do a proper review with everything else going on this Fall. I also don't have a student to delegate.
I cannot review either but my colleague Fan Zhang can review. @zhangfanmark
@whedon add @lbrea as reviewer
OK, @lbrea is now a reviewer
@whedon add @zhangfanmark as reviewer
OK, @zhangfanmark is now a reviewer
@whedon start review
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2705.
Submitting author: @mathpluscode (Yunguan Fu) Repository: https://github.com/DeepRegNet/DeepReg Version: v0.1.0 Editor: @Kevin-Mattheus-Moerman Reviewers: @ethanwharris, @lbrea, @zhangfanmark Managing EiC: Kristen Thyng
:warning: JOSS reduced service mode :warning:
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 @mathpluscode. Currently, there isn't an JOSS editor assigned to your paper.
The author's suggestion for the handling editor is @arokem.
@mathpluscode 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: