[PRE REVIEW]: MRdataset: A unified and user-friendly interface to medical imaging datasets

[editorialbot]

Submitting author: !--author-handle-->@sinhaharsh<!--end-author-handle-- (Harsh Sinha) Repository: https://github.com/Open-Minds-Lab/MRdataset Branch with paper.md (empty if default branch): joss Version: 0.33 Editor: !--editor-->@mstimberg<!--end-editor-- Reviewers: @htwangtw, @djmannion Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1b9ca51a9cc20b3e98f26e598c09c381"><img src="https://joss.theoj.org/papers/1b9ca51a9cc20b3e98f26e598c09c381/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1b9ca51a9cc20b3e98f26e598c09c381/status.svg)](https://joss.theoj.org/papers/1b9ca51a9cc20b3e98f26e598c09c381)

Author instructions

Thanks for submitting your paper to JOSS @sinhaharsh. Currently, there isn't a JOSS editor assigned to your paper.

@sinhaharsh if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1251.5 files/s, 135464.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           22            574           1048           1719
XML                               1              0              0            378
reStructuredText                 11            141            100            189
TeX                               1             12              0            124
Jupyter Notebook                  1              0            399            120
make                              2             28              6             78
YAML                              2              7              9             77
JSON                              2              0              0             71
TOML                              1              8              0             56
Markdown                          2             25              0             50
INI                               1              5              3             30
DOS Batch                         1              8              1             27
Bourne Again Shell                1              5              0              5
HTML                              1              0              0              1
--------------------------------------------------------------------------------
SUM:                             49            813           1566           2925
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 971

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.7795644 is OK
- 10.21105/joss.01294 is OK
- 10.3389/fninf.2017.00017 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

PyBIDS: Python tools for BIDS datasets Submitting author: @tyarkoni Handling editor: @cMadan (Active) Reviewers: @grlee77 Similarity score: 0.8559

PyQMRI: An accelerated Python based Quantitative MRI toolbox Submitting author: @maieroli2010 Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @grlee77, @agahkarakuzu, @DARSakthi Similarity score: 0.8475

CleanX: A Python library for data cleaning of large sets of radiology images Submitting author: @drcandacemakedamoore Handling editor: @cMadan (Active) Reviewers: @henrykironde, @anki-xyz Similarity score: 0.8427

Virtual Scanner: MRI on a Browser Submitting author: @imr-framework Handling editor: @arokem (Retired) Reviewers: @nstikov, @vsoch, @mathieuboudreau Similarity score: 0.8404

Imagedata: A Python library to handle medical image data in NumPy array subclass Series Submitting author: @erling6232 Handling editor: @galessiorob (Active) Reviewers: @mwegrzyn, @hsang Similarity score: 0.8395

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@sinhaharsh thanks for this submission. I am the AEiC on this track and here to help with initial steps. I have just added the query-scope label here. This is to trigger a scope review by the editorial board. I have done this because I need some help to determine if this work is in scope. In particular some domain experts should weigh in to see if the scientific research functionality provided here is significant enough to warrant a JOSS publication. The scope review should take about 2 weeks to complete.

[raamana]

Thanks @Kevin-Mattheus-Moerman for facilitating the review of our paper. We appreciate the time and effort of you and the reviewers.

[sinhaharsh]

@Kevin-Mattheus-Moerman Thanks for guiding us through this review! We're excited about the upcoming review process at JOSS.

[raamana]

Just a gentle reminder!

[raamana]

Hi @Kevin-Mattheus-Moerman, did the query for scope get triggered properly?

I am quite biased as a developer and an author, but I can't see why our paper would be out of scope, as I'd think any active informatics researchers in neuroscience world would agree with us :)

[raamana]

Hi @Kevin-Mattheus-Moerman , can you update us on whats happening? its been over 5 weeks now (although I do understand there were some holiday breaks etc). if we don't hear from you in the next week or two (which would disappoint me greatly as someone who published 4 papers in JOSS before), we would have to explore alternative venues.

[Kevin-Mattheus-Moerman]

@raamana @sinhaharsh apologies for the delay. With the holidays, and the start of semester for many, this scope review has taken longer than expected. Having said that I should also apologize for not responding/providing and update sooner. Based on the scope review from the editorial board so far I believe we can proceed and say this work may be in scope. I will remove the query scope label now, and will start by inviting an editor. One concern was that this work may not offer more than a wrapper around pydicom. It may be helpful if you responded here with information around how your work goes beyond that.

[Kevin-Mattheus-Moerman]

@editorialbot invite @emdupre as editor

[editorialbot]

Invitation to edit this submission sent!

[raamana]

Thanks for the response - as out of domain editor, I appreciate your confusion and questions, and we hope we have sufficiently answered them in short paper we submitted for review: https://github.com/Open-Minds-Lab/MRdataset/blob/joss/joss/paper.pdf

MRDataset was developed to reduce the complexity in dealing with large variations in dataset formats! I repeat, it is NOT file format (like DICOM), but a DATASET format like BIDS and other more complex and esoteric structures in use in the neuroscience world. The Base classes (such as BaseMRDataset) and the derived classes we designed ( such as DicomDataset) are aimed to offer a uniform interface to an user without expertise in dealing with variations in these DATASET formats (again, not file formats). Other than pybids (which focuses exclusively on BIDS), we are not aware of other libraries doing this (we'd be happy to cover other libraries if we missed them). Perhaps we didn't communicate that well enough in our paper and we hope to revise it during the review process.

Besides the unified interface at the dataset level, though physics-based representation of individual MRI physics parameters (via protocol ), we offer deep cross-vendor conversion (across Siemens, GE, Philips etc) for MRI physics parameter units and values, that is essential for the protocol compliance research based on over 20 open datasets that MRdataset enables.

PS: also, regarding the concern that "this work may not offer more than a wrapper around pydicom", the same accusation can be laid against pybids and imagedata (and even nibabel), but talk to any of the neuroinformatics researchers, they would make it clear how useful and critical these libraries are.

[Kevin-Mattheus-Moerman]

@raamana thanks for getting back to me on that. My domain is indeed different (However, I have worked on MRI sequences, and did in the past implement a DICOM/analyze importer). The comments I posted originated from points raised by other editorial board members who are closer aligned with this domain. Either way, we are passed this now. I think the information you provide is helpful. We are now waiting for this to receive a handling editor. I'll ping the one I invited now again.

[Kevin-Mattheus-Moerman]

@emdupre do you think you could help edit this one? :wave:

[emdupre]

Hi @Kevin-Mattheus-Moerman, thanks for the invitation ! I needed to re-check the JOSS COI policy on for both of the newly invited submissions.

For this one, I have a few authorships with the senior author, the most recent having been accepted this month, though this 2021 paper would also qualify under the COI policy. As these were large efforts in which Dr Raamana and I had minimal interaction, however, I believe that I can review this submission impartially. I'll leave, though, the final decision up to you !

[Kevin-Mattheus-Moerman]

@emdupre those would quality as potential/perceived COIs so I'll have to recruit an alternative editor. Thanks for reporting that.

[Kevin-Mattheus-Moerman]

@editorialbot invite @mstimberg as editor

[editorialbot]

Invitation to edit this submission sent!

[mstimberg]

@editorialbot assign me as editor

Happy to edit the submission!

[editorialbot]

Assigned! @mstimberg is now the editor

[mstimberg]

:wave: @sinhaharsh, @raamana I will facilitate the review of your paper/software as the editor. The first step will be to find reviewers, so I will start contacting potential reviewers over mail later today. If you have any suggestions for potential reviewers, then please mention them here in this thread (without tagging them with an @).

[raamana]

Thank you Marcel for accepting and helping facilitate the review! I will try to come up with some names, but I must admit most of the names that come to my mind right now (those who'd appreciate what this has to offer) are folks (like @emdupre ) I've collaborated with in some form over big community projects or small hackathon projects

great reviewers would be potential future users, those that actually have reasonable experience in acquiring MRI scans on physical scanners in the real-world (not just processing them after they shared in BIDS format etc) and know the issues with managing DICOM data

[raamana]

Hi Marcel and Kevin, back in the day when JOSS started, there was an excel of volunteers willing to review. Does JOSS still maintain it? also, do you have any tools for automatic checks of COI?

[mstimberg]

Hi Marcel and Kevin, back in the day when JOSS started, there was an excel of volunteers willing to review. Does JOSS still maintain it? also, do you have any tools for automatic checks of COI?

The old sheet has been replaced by this system here: https://reviewers.joss.theoj.org/reviewers AFAIK, we don't have any automatic system for checking COIs.

I found two reviewers that agreed to review, though. I will assign them now and we can start the review process :rocket:

[mstimberg]

@editorialbot assign @htwangtw as reviewer

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[mstimberg]

@editorialbot add @htwangtw as reviewer

[editorialbot]

@htwangtw added to the reviewers list!

[mstimberg]

@editorialbot add @djmannion as reviewer

[editorialbot]

@djmannion added to the reviewers list!

[mstimberg]

Many thanks @htwangtw and @djmannion for agreeing to help out as reviewers ! I will now start the official reviewing process, which will close this issue and open the review issue, where the actual review will take place. See you over there :wave:

[mstimberg]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6269.

[raamana]

thanks Marcel, Hao and Damien! :)