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[REVIEW]: The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images #3920

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@antoinevacavant<!--end-author-handle-- (Antoine Vacavant) Repository: https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation Branch with paper.md (empty if default branch): Version: 1.0.2 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @lassoan, @deepakri201 Archive: 10.5281/zenodo.6513517

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Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/999c4fe176099cce249b99ddea1b5bc5/status.svg)](https://joss.theoj.org/papers/999c4fe176099cce249b99ddea1b5bc5)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@lassoan & @deepakri201, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @deepakri201

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lassoan, @deepakri201 it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Wordcount for paper.md is 888

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (261.2 files/s, 66836.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21           1251           1711           3540
Markdown                         2             74              0            174
TeX                              1              8              0             64
CMake                            3             11             14             61
-------------------------------------------------------------------------------
SUM:                            27           1344           1725           3839
-------------------------------------------------------------------------------

Statistical information for the repository '163251f2e9cb709eef29519d' was
gathered on 2021/11/17.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Lucie Macron                     2           305             14            1.59
Thibault Pelletier             109         12976           6765           98.41

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
Lucie Macron                 47           15.4          4.7                8.51
Thibault Pelletier         6455           49.7         17.6               13.90
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1007/978-1-4614-7657-3_19 may be a valid DOI for title: 3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support
- 10.1007/s11517-008-0420-1 may be a valid DOI for title: An image-based modeling framework for patient-specific computational hemodynamics
- 10.1109/ipta50016.2020.9286658 may be a valid DOI for title: A Time-dependent joint segmentation and registration model: Applications to longitudinal registration of hepatic DCE-MRI sequences
- 10.3390/app11114895 may be a valid DOI for title: Segmentation of liver anatomy by combining 3-D U-Net approaches
- 10.1109/icpr48806.2021.9412362 may be a valid DOI for title: Vesselness filters: A survey with benchmarks applied to liver imaging

INVALID DOIs

- None
whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

deepakri201 commented 2 years ago

Hi @antoinevacavant, could you please confirm that the installation instructions you have provided are correct? For instance, I had to add the two subfolders (RVXLiverSegmentation and RVXLiverSegmentationEffect) in Edit > Application Settings > Modules > Additional module paths, instead of the main directory as you indicated. Thank you!

antoinevacavant commented 2 years ago

Hi @deepakri201 yes the documentation contains an old instruction about this main directory. Sorry for the confusion. You should add both paths to RVXLiverSegmentation and RVXLiverSegmentationEffect indeed. We will update the readme file for making this point clear.

whedon commented 2 years ago

:wave: @lassoan, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @deepakri201, please update us on how your review is going (this is an automated reminder).

deepakri201 commented 2 years ago

Hi @antoinevacavant, I believe there are a few things to be checked for the paper:

antoinevacavant commented 2 years ago

Hi @deepakri201 thanks a lot for your feedback. @Kevin-Mattheus-Moerman should I revise the paper now, or wait for any other review?

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant best wishes for 2022! :tada:

You can start addressing issues as they come in and as you see fit.

antoinevacavant commented 2 years ago

@Kevin-Mattheus-Moerman thanks a lot, all my best wishes for 2022! ;) I will address those issues asap.

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant how are you getting on? Could you give us an update?

antoinevacavant commented 2 years ago

@Kevin-Mattheus-Moerman thanks for your message, I am editing the .md and .bib files of our paper. Once they are ready, I suppose I have to:

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant Please push all changes to the branch under review. Once done you can recompile the paper here by calling the following in a comment: @whedon generate pdf or @whedon generate pdf from branch branchName

Once you do the above you are done, so there is no need to resubmit.

antoinevacavant commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

antoinevacavant commented 2 years ago

@Kevin-Mattheus-Moerman We have revised/generated the paper, and solved a first issue for the repo. We need more time to solve the second issue (tutorial video, etc.). Would it be possible to continue the review process despite this unsolved issue? Thanks.

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant can you clarify what issue is unresolved? Can you link to it here?

Also can you clarify if you addressed @deepakri201 's points above :point_up: about the statement of need and references?

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant also note the reviews for JOSS are quite fluid so issues can be resolved simultaneously or incrementally / one at a time, irrespective of what reviewer raised them. So the review remains "ongoing" until all points for all reviewers are addressed, So there are no review "rounds" like for a classic journal. Does this help clarify things?

antoinevacavant commented 2 years ago

@Kevin-Mattheus-Moerman This issue is solved: https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/2 (Community guidelines) This one is still unresolved: https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/1 And we addressed the points raised by @deepakri201 in the new version of the paper (statement of need + references).

Kevin-Mattheus-Moerman commented 2 years ago

@lassoan I hope you are doing well. Are you able to provide update on progress on this review? Thanks again for your help.

Kevin-Mattheus-Moerman commented 2 years ago

@lassoan I hope you are well. Can you provide an update on the review? Thanks.

Kevin-Mattheus-Moerman commented 2 years ago

@deepakri201 can you review the changes made? :point_up: Also I've noticed you've one box unticked. Can you comment if anything is still missing or needs to be addressed? Thanks.

Kevin-Mattheus-Moerman commented 2 years ago

@lassoan I hope you are well. Can you provide an update on the review? Thanks.

deepakri201 commented 2 years ago

I left the one box unticked because I believe there still are a few comments to be addressed here: https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/1

Kevin-Mattheus-Moerman commented 2 years ago

@deepakri201 thanks for the update.

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant @Thibault-Pelletier how are you getting on addressing @deepakri201 's comment on documentation?

Kevin-Mattheus-Moerman commented 2 years ago

@lassoan thanks again for your help with this review. I hope you can pick up the review at this point. Let me know if you have any questions.

lassoan commented 2 years ago

I've reviewed the paper, tested the software, and went through the checklist. All checks passed but I could not tick the items (probably because I did not accept the invitation in time and now the invitation is expired).

I had some difficulty with testing vessel segmentation part because I'm not familiar enough with liver vasculature, but the feature seemed to work. Fixing @deepakri201's comments at https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/1 will address this issue.

I've added a few suggestions about improving installation instructions: https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/4

Kevin-Mattheus-Moerman commented 2 years ago

@lassoan thanks.

We have also since moved onto a different editorial bot system. To fix your box ticking issue, can you call the following in a comment: @editorialbot generate my checklist

lassoan commented 2 years ago

Review checklist for @lassoan

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Kevin-Mattheus-Moerman commented 2 years ago

Thanks @lassoan! Since all your boxes are now ticked for you, could you confirm if you are happy to recommend acceptance?

lassoan commented 2 years ago

Yes, I would recommend acceptance. Issues https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/1 and https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation/issues/4 would be nice to be fixed soon but the current state of things is already acceptable for me.

Kevin-Mattheus-Moerman commented 2 years ago

@lassoan okay. Thanks again for your help here!

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1007/978-1-4614-7657-3_19 may be a valid DOI for title: 3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support
- 10.1007/s11517-008-0420-1 may be a valid DOI for title: An image-based modeling framework for patient-specific computational hemodynamics
- 10.1109/ipta50016.2020.9286658 may be a valid DOI for title: A Time-dependent joint segmentation and registration model: Applications to longitudinal registration of hepatic DCE-MRI sequences
- 10.3390/app11114895 may be a valid DOI for title: Segmentation of liver anatomy by combining 3-D U-Net approaches
- 10.1109/icpr48806.2021.9412362 may be a valid DOI for title: Vesselness filters: A survey with benchmarks applied to liver imaging
- 10.1016/j.diii.2019.05.008 may be a valid DOI for title: Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation
- 10.1016/j.crad.2013.12.021 may be a valid DOI for title: CT volumetry of the liver: where does it stand in clinical practice?

INVALID DOIs

- None
Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant apologies for the delay in processing this paper. Since the reviewers are now happy to recommend acceptance we will proceed now to process this work for acceptance in JOSS. I have now also proofread you paper and below are some final points to work on:

Once you've completed the above, please call @editorialbot generate pdf to update the paper.

antoinevacavant commented 2 years ago

Hi @Kevin-Mattheus-Moerman thanks a lot for this good news ;)

antoinevacavant commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1007/978-1-4614-7657-3_19 may be a valid DOI for title: 3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support
- 10.1007/s11517-008-0420-1 may be a valid DOI for title: An image-based modeling framework for patient-specific computational hemodynamics
- 10.1109/ipta50016.2020.9286658 may be a valid DOI for title: A Time-dependent joint segmentation and registration model: Applications to longitudinal registration of hepatic DCE-MRI sequences
- 10.3390/app11114895 may be a valid DOI for title: Segmentation of liver anatomy by combining 3-D U-Net approaches
- 10.1109/icpr48806.2021.9412362 may be a valid DOI for title: Vesselness filters: A survey with benchmarks applied to liver imaging
- 10.1016/j.diii.2019.05.008 may be a valid DOI for title: Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation
- 10.1016/j.crad.2013.12.021 may be a valid DOI for title: CT volumetry of the liver: where does it stand in clinical practice?

INVALID DOIs

- None
Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant Thanks for making those changes. Some more minor things:

antoinevacavant commented 2 years ago

@Kevin-Mattheus-Moerman Well I forgot to update correctly the .bib file ;( And last typo is corrected

antoinevacavant commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left: