[PRE REVIEW]: BrainDiffusion: A Python package for brain anatomic connectivity matrix.

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@CoderNoMercy<!--end-author-handle-- (Zheyu Wen) Repository: https://github.com/CoderNoMercy/BrainDiffusion Branch with paper.md (empty if default branch): Version: v0.1.5 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (511.3 files/s, 98246.9 lines/s)
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Language                      files          blank        comment           code
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Python                            9            624            471           1212
TeX                               1             20              0            217
Markdown                          2             28              0             81
YAML                              1              1              4             18
Bourne Again Shell                1              3              7              4
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SUM:                             14            676            482           1532
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1204

editorialbot commented 1 year ago

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

OK DOIs

- 10.1227/00006123-199604000-00026 is OK

MISSING DOIs

- 10.1016/0167-8191(96)00024-5 may be a valid DOI for title: A high-performance, portable implementation of the MPI message passing interface standard

INVALID DOIs

- https://doi.org/10.1016/j.neuroimage.2007.10.060 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/nbm.1579 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2019.116137 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41467-020-15701-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nature12481 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41591-021-01309-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jmps.2018.10.013 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.48550/arXiv.2106.06016 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/BF02127704 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jmri.27188 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41583-018-0071-7 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.1910340409 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.22159 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2021.118870 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1155/2012/412512 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.clineuro.2014.06.009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s00285-015-0888-x is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 year 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 1 year ago

@CoderNoMercy thanks for this submission to JOSS. I am the AEiC for this track and here to help with initial steps. Below are some points that require your attention before we proceed:

[ ] Please check the above potentially missing/invalid DOIs :point_up:. You can try to address it and call @editorialbot check references here to check the DOIs again.
[ ] Please extend the basic description of the project in your README, a short e.g. 1 or 2 paragraph description of the project would be great.
[ ] Please add basic contributing guidelines to your project. I simple way of doing this is a section in your README. A more complete approach would be to have a dedicated CONTRIBUTING.md file you link to in the README. Examples for such a file are described here for instance: https://contributing.md/example/

Note, I have just triggered a scope review by the editorial board. This is because I need some help to determine if this work is in scope for JOSS. In particular it looks like the project, in terms of lines of code, is rather small. Furthermore, the project appears rather new (~3 months) with contributions by one author and no posted issues yet. The scope review will determine if this work is deemed to conform to our substantial scholarly effort criteria. Typically this review will take about 2-3 weeks to complete.

Zheyu-Wen commented 1 year ago

Hi Kevin,

Thanks for your email! I will address the points you mentioned.

In reference to the scope review, we have been diligently working on the development of this software for over a year, and it was recently made available on Github. Prior to its public release, the software underwent several iterations and versions. It played a pivotal role in our accepted paper for the MICCAI workshop in 2023, titled 'A Two-Species Model for Abnormal Tau Dynamics in Alzheimer's Disease,' and is currently in use for our upcoming paper in IEEE Transactions on Medical Imaging.

To ensure clarity and conciseness, we extracted the essential components of the software from a larger codebase. We appreciate your understanding of our intentions and eagerly await your feedback.

Kevin Mattheus Moerman @.***> 于2023年11月7日周二 08:27写道：

@CoderNoMercy https://github.com/CoderNoMercy thanks for this submission to JOSS. I am the AEiC for this track and here to help with initial steps. Below are some points that require your attention before we proceed:

Please check the above potentially missing/invalid DOIs ☝️. You can try to address it and call @editorialbot check references here to check the DOIs again.

Please extend the basic description of the project in your README, a short e.g. 1 or 2 paragraph description of the project would be great.

Please add basic contributing guidelines to your project. I simple way of doing this is a section in your README. A more complete approach would be to have a dedicated CONTRIBUTING.md file you link to in the README. Examples for such a file are described here for instance: https://contributing.md/example/

Note, I have just triggered a scope review by the editorial board. This is because I need some help to determine if this work is in scope for JOSS. In particular it looks like the project, in terms of lines of code, is rather small. Furthermore, the project appears rather new (~3 months) with contributions by one author and no posted issues yet. The scope review will determine if this work is deemed to conform to our substantial scholarly effort criteria https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort. Typically this review will take about 2-3 weeks to complete.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6029#issuecomment-1798645997, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYQVMAKSZR2GAMKVQXNJILYDJAMDAVCNFSM6AAAAAA7BH3AP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJYGY2DKOJZG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- University of Michigan, Ann Arbor Signal, image processing and machine learning major Personal Website: https://zheyw.netlify.app/ GitHub: https://github.com/CoderNoMercy

Zheyu-Wen commented 12 months ago

@editorialbot check references

The Open Journals editorial robot @.***> 于2023年11月7日周二 08:06写道：

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

OK DOIs

10.1227/00006123-199604000-00026 is OK

MISSING DOIs

10.1016/0167-8191(96)00024-5 may be a valid DOI for title: A high-performance, portable implementation of the MPI message passing interface standard

INVALID DOIs

https://doi.org/10.1016/j.neuroimage.2007.10.060 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1002/nbm.1579 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1016/j.neuroimage.2019.116137 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1038/s41467-020-15701-2 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1038/nature12481 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1038/s41591-021-01309-6 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1016/j.jmps.2018.10.013 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.48550/arXiv.2106.06016 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1007/BF02127704 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1002/jmri.27188 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1038/s41583-018-0071-7 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1002/mrm.1910340409 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1002/mrm.22159 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1016/j.neuroimage.2021.118870 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1155/2012/412512 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1016/j.clineuro.2014.06.009 is INVALID because of 'https://doi.org/' prefix

https://doi.org/10.1007/s00285-015-0888-x is INVALID because of 'https://doi.org/' prefix

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6029#issuecomment-1798591470, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYQVMEVVE3LY6TFGSSQPXTYDI55BAVCNFSM6AAAAAA7BH3AP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJYGU4TCNBXGA . You are receiving this because you were mentioned.Message ID: @.***>

-- University of Michigan, Ann Arbor Signal, image processing and machine learning major Personal Website: https://zheyw.netlify.app/ GitHub: https://github.com/CoderNoMercy

editorialbot commented 12 months ago

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

OK DOIs

- 10.1016/j.neuroimage.2007.10.060 is OK
- 10.1002/nbm.1579 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.1038/s41467-020-15701-2 is OK
- 10.1038/nature12481 is OK
- 10.1038/s41591-021-01309-6 is OK
- 10.1016/j.jmps.2018.10.013 is OK
- 10.1093/comjnl/7.2.149 is OK
- 10.1007/BF02127704 is OK
- 10.1002/jmri.27188 is OK
- 10.1038/s41583-018-0071-7 is OK
- 10.1002/mrm.1910340409 is OK
- 10.1002/mrm.22159 is OK
- 10.1016/j.neuroimage.2021.118870 is OK
- 10.1155/2012/412512 is OK
- 10.1016/j.clineuro.2014.06.009 is OK
- 10.1227/00006123-199604000-00026 is OK
- 10.1007/s00285-015-0888-x is OK
- 10.1002/jmri.1076 is OK
- 10.1016/0167-8191(96)00024-5 is OK

MISSING DOIs

- None

INVALID DOIs

- 0.48550/arXiv.2106.06016 is INVALID

Zheyu-Wen commented 12 months ago

@editorialbot check references

The Open Journals editorial robot @.***> 于2023年11月7日周二 20:47写道：

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

OK DOIs

10.1016/j.neuroimage.2007.10.060 is OK

10.1002/nbm.1579 is OK

10.1016/j.neuroimage.2019.116137 is OK

10.1038/s41467-020-15701-2 is OK

10.1038/nature12481 is OK

10.1038/s41591-021-01309-6 is OK

10.1016/j.jmps.2018.10.013 is OK

10.1093/comjnl/7.2.149 is OK

10.1007/BF02127704 is OK

10.1002/jmri.27188 is OK

10.1038/s41583-018-0071-7 is OK

10.1002/mrm.1910340409 is OK

10.1002/mrm.22159 is OK

10.1016/j.neuroimage.2021.118870 is OK

10.1155/2012/412512 is OK

10.1016/j.clineuro.2014.06.009 is OK

10.1227/00006123-199604000-00026 is OK

10.1007/s00285-015-0888-x is OK

10.1002/jmri.1076 is OK

10.1016/0167-8191(96)00024-5 is OK

MISSING DOIs

None

INVALID DOIs

0.48550/arXiv.2106.06016 is INVALID

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6029#issuecomment-1800923933, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYQVMCYV3MEYSR65FDAIN3YDLXCNAVCNFSM6AAAAAA7BH3AP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBQHEZDGOJTGM . You are receiving this because you were mentioned.Message ID: @.***>

-- University of Michigan, Ann Arbor Signal, image processing and machine learning major Personal Website: https://zheyw.netlify.app/ GitHub: https://github.com/CoderNoMercy

editorialbot commented 12 months ago

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

OK DOIs

- 10.1016/j.neuroimage.2007.10.060 is OK
- 10.1002/nbm.1579 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.1038/s41467-020-15701-2 is OK
- 10.1038/nature12481 is OK
- 10.1038/s41591-021-01309-6 is OK
- 10.1016/j.jmps.2018.10.013 is OK
- 10.1093/comjnl/7.2.149 is OK
- 10.1007/BF02127704 is OK
- 10.1002/jmri.27188 is OK
- 10.1038/s41583-018-0071-7 is OK
- 10.1002/mrm.1910340409 is OK
- 10.1002/mrm.22159 is OK
- 10.1016/j.neuroimage.2021.118870 is OK
- 10.1155/2012/412512 is OK
- 10.1016/j.clineuro.2014.06.009 is OK
- 10.1227/00006123-199604000-00026 is OK
- 10.1007/s00285-015-0888-x is OK
- 10.1002/jmri.1076 is OK
- 10.1016/0167-8191(96)00024-5 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1109/TMI.2022.3221913. is INVALID

Zheyu-Wen commented 12 months ago

@editorialbot check references

The Open Journals editorial robot @.***> 于2023年11月7日周二 20:50写道：

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

OK DOIs

10.1016/j.neuroimage.2007.10.060 is OK

10.1002/nbm.1579 is OK

10.1016/j.neuroimage.2019.116137 is OK

10.1038/s41467-020-15701-2 is OK

10.1038/nature12481 is OK

10.1038/s41591-021-01309-6 is OK

10.1016/j.jmps.2018.10.013 is OK

10.1093/comjnl/7.2.149 is OK

10.1007/BF02127704 is OK

10.1002/jmri.27188 is OK

10.1038/s41583-018-0071-7 is OK

10.1002/mrm.1910340409 is OK

10.1002/mrm.22159 is OK

10.1016/j.neuroimage.2021.118870 is OK

10.1155/2012/412512 is OK

10.1016/j.clineuro.2014.06.009 is OK

10.1227/00006123-199604000-00026 is OK

10.1007/s00285-015-0888-x is OK

10.1002/jmri.1076 is OK

10.1016/0167-8191(96)00024-5 is OK

MISSING DOIs

None

INVALID DOIs

10.1109/TMI.2022.3221913. is INVALID

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6029#issuecomment-1800925964, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYQVMBCZD5N73B23UDEWPLYDLXONAVCNFSM6AAAAAA7BH3AP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBQHEZDKOJWGQ . You are receiving this because you were mentioned.Message ID: @.***>

-- University of Michigan, Ann Arbor Signal, image processing and machine learning major Personal Website: https://zheyw.netlify.app/ GitHub: https://github.com/CoderNoMercy

editorialbot commented 12 months ago

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

OK DOIs

- 10.1016/j.neuroimage.2007.10.060 is OK
- 10.1002/nbm.1579 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.1038/s41467-020-15701-2 is OK
- 10.1038/nature12481 is OK
- 10.1038/s41591-021-01309-6 is OK
- 10.1016/j.jmps.2018.10.013 is OK
- 10.1109/TMI.2022.3221913 is OK
- 10.1093/comjnl/7.2.149 is OK
- 10.1007/BF02127704 is OK
- 10.1002/jmri.27188 is OK
- 10.1038/s41583-018-0071-7 is OK
- 10.1002/mrm.1910340409 is OK
- 10.1002/mrm.22159 is OK
- 10.1016/j.neuroimage.2021.118870 is OK
- 10.1155/2012/412512 is OK
- 10.1016/j.clineuro.2014.06.009 is OK
- 10.1227/00006123-199604000-00026 is OK
- 10.1007/s00285-015-0888-x is OK
- 10.1002/jmri.1076 is OK
- 10.1016/0167-8191(96)00024-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 11 months ago

👋 @CoderNoMercy - can you explain a bit more about this?

To ensure clarity and conciseness, we extracted the essential components of the software from a larger codebase.

What is the larger codebase? Is it yours as well? Has it previously been reviewed/published?

Zheyu-Wen commented 11 months ago

Hi Danial 👋,

Thanks for your email! In response to your question, we have developed a workflow aimed at investigating the mechanism of misfolded tau propagation in Alzheimer's Disease. This workflow encompasses several components, including graph creation from brain data (the current focus of our JOSS code), observation data preprocessing, a tool for solving the inverse problem of the computational model of tau, and visualization. These components constitute our original codes, which have not been previously published or reviewed.

In our JOSS submission, we delve into the details of how we construct connectivity between brain regions of interest (ROIs) to form a graph on the brain domain. This code extends beyond Alzheimer's Disease research, with potential applications in neuroscience and clinical neuroimaging that require connectivity information of brain structures. By publishing this tool through JOSS, we aim to provide an alternative resource for researchers in these fields.

We hope this information provides a clearer understanding of our work! Please feel free to reach out if you have any further questions.

Daniel S. Katz @.***> 于2023年11月13日周一 07:41写道：

👋 @CoderNoMercy https://github.com/CoderNoMercy - can you explain a bit more about this?

To ensure clarity and conciseness, we extracted the essential components of the software from a larger codebase.

What is the larger codebase? Is it yours as well? Has it previously been reviewed/published?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6029#issuecomment-1808187141, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYQVMFIR2EKARK25CM4VTLYEIPRBAVCNFSM6AAAAAA7BH3AP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBYGE4DOMJUGE . You are receiving this because you were mentioned.Message ID: @.***>

-- University of Michigan, Ann Arbor Signal, image processing and machine learning major Personal Website: https://zheyw.netlify.app/ GitHub: https://github.com/CoderNoMercy

danielskatz commented 11 months ago

Can I ask why you're not submitting the full set of software to JOSS?

Kevin-Mattheus-Moerman commented 11 months ago

@CoderNoMercy :wave: could you respond to Dan's questions here? Thanks

Zheyu-Wen commented 11 months ago

Hi Daniel and Kevin,

I'm really sorry for the late reply! Last week I chat with my supervisor Dr. Biros. My supervisor planed to draft the reply by himself. But he was in multiple travels and this week is Thanksgiving. I will urge him next Monday in our personal meeting. Would it be possible to reply to you next week? Great thanks for your understanding!!

Kevin Mattheus Moerman @.***> 于2023年11月23日周四 04:16写道：

@CoderNoMercy https://github.com/CoderNoMercy 👋 could you respond to Dan's questions here? Thanks

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6029#issuecomment-1824126049, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMYQVMEP3NGQU6POF2XUH3DYF4O7LAVCNFSM6AAAAAA7BH3AP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRUGEZDMMBUHE . You are receiving this because you were mentioned.Message ID: @.***>

-- University of Michigan, Ann Arbor Signal, image processing and machine learning major Personal Website: https://zheyw.netlify.app/ GitHub: https://github.com/CoderNoMercy

Zheyu-Wen commented 11 months ago

Dear Daniel and Kevin,

Thank you for your inquiry! The code submitted to JOSS represents a versatile framework for computing structural connectivity matrices in an innovative manner. The code is stand-alone and doesn't have any other components other than Python dependencies. In our paper, we explain the significance of reconstructing white matter fiber connectivity: it finds applications in brain cancers, brain activity studies, and neurodegenerative diseases. In our group we are using it for Alzheimer's disease but also brain tumor analysis ([1],[2],[3]), but these are separate projects. Our code is highly non-trivial as it involves solving several 3D anisotropic, variable coefficient Poisson problems driven by medical imaging data; and it is parallelized to support MPI and GPUs. We devoted a year to the design, verification, and optimization of this scheme, and we sincerely hope that our efforts are recognized. Feel free to reach out if you have further questions about our work.

Many thanks!

[1] https://sites.google.com/view/mtsailelaf-2023/program-and-registration?authuser=0 A Two-Species Model for Abnormal Tau Dynamics in Alzheimer's Disease [2] https://ieeexplore.ieee.org/abstract/document/9197710 [3] https://arxiv.org/abs/2007.01236

Best regards, Zheyu

Kevin-Mattheus-Moerman commented 11 months ago

@CoderNoMercy can you please answer Dan's questions clearly/directly. I am not sure I can see a response clearly in your comments.

What is the larger codebase? Is it yours as well? Has it previously been reviewed/published?
Why are you not submitting the full set of software to JOSS?

Zheyu-Wen commented 11 months ago

I apologize for the confusion in my previous explanation.

1) "What is the larger codebase? Is it yours as well? Has it previously been reviewed/published?" There is no larger codebase. But as we mentioned many other downstream applications can use the proposed algorithm.

2) "Why are you not submitting the full set of software to JOSS?" We're submitting the entire codebase related to reconstructing white matter tractography in the brain. Nothing is left out.

Kevin-Mattheus-Moerman commented 11 months ago

@Zheyu-Wen thanks for the clarification

Kevin-Mattheus-Moerman commented 11 months ago

@CoderNoMercy the editorial board has determined this work is not in scope as it stands. The code base is rather small with rather limited functionality around diffusion/MRI. On top of this, the project lacks maturity in terms of well developed and automated testing, and thorough documentation. The documentation currently appears limited to the README and a folder containing some examples.

We will now proceed to reject this submission. Note that this conclusion does not mean the work is of a poor quality, or not useful, it merely means that as it stands the work is not in scope for JOSS.

If you would like to consider resubmitting this work, we recommend that you first of all critically review how this software functionality fits in with the rest of the ecosystem you describe. Perhaps it can be merged or combined with other functionality/code into a larger project that covers more aspects. Secondly the project should be extended with automated testing of all functionality. Thirdly, detailed dedicated documentation should be added. If examples do not include visualisations at present it is also recommended to add this (or to add this capability to the project where possible).

Kevin-Mattheus-Moerman commented 11 months ago

@editorialbot reject

editorialbot commented 11 months ago

Paper rejected.

openjournals / joss-reviews

[PRE REVIEW]: BrainDiffusion: A Python package for brain anatomic connectivity matrix. #6029

Status