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[REVIEW]: Longitudinal stability of brain and spinal cord quantitative MRI measures #18

Closed roboneuro closed 1 year ago

roboneuro commented 1 year ago

Submitting author: !--author-handle-->@mathieuboudreau<!--end-author-handle-- (Mathieu Boudreau) Repository: https://github.com/courtois-neuromod/anat-processing-paper Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@agahkarakuzu<!--end-editor-- Reviewers: !--reviewers-list-->@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00018 Repository archive: 10.5281/zenodo.10038872 Data archive: 10.5281/zenodo.10038874 Book archive: 10.5281/zenodo.10038870 Docker archive: 10.5281/zenodo.10038876

Status

status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d"><img src="https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d/status.svg)](https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d)

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

@agahkarakuzu, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@roboneuro generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @agahkarakuzu 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 ✨

Checklists

@agahkarakuzu, please create your checklist typing: @roboneuro generate my checklist

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 1beaf75d Last updated: 2023-10-20 08:12:09 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. ℹ️ Please read and confirm the following:

    [!IMPORTANT]
    We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.

    • [x] I, the submitting author, confirm that I have read the note above.

  5. ♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

    For the technical screener

    Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

    :warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

agahkarakuzu commented 1 year ago

@mathieuboudreau you can follow the latest extended pdf build instructions to update the paper.md and paper.bib 👇

I fixed some typos 👇

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 4965585b Last updated: 2023-10-20 08:54:14 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. ℹ️ Please read and confirm the following:

    [!IMPORTANT]
    We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.

    • [ ] I, the submitting author, confirm that I have read the note above.

  5. ♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

    For the technical screener

    Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

    :warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

agahkarakuzu commented 1 year ago

@roboneuro recommend-accept

roboneuro commented 1 year ago 
Attempting dry run of processing paper acceptance...
roboneuro commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.54294/uvnhin is OK
- 10.1002/mrm.29216 is OK
- 10.1016/j.nicl.2021.102849 is OK
- 10.1109/MCSE.2021.3052101 is OK
- 10.1002/cmr.a.21357 is OK
- 10.1016/j.cortex.2008.05.004 is OK
- 10.1002/mrm.22423 is OK
- 10.1038/s41596-021-00588-0 is OK
- 10.1038/s41597-021-01044-0 is OK
- 10.1002/mrm.28020 is OK
- 10.1016/j.nicl.2017.07.020 is OK
- 10.1073/pnas.95.4.1834 is OK
- 10.1016/j.neuroimage.2016.10.009 is OK
- 10.1016/j.neuroimage.2017.10.041 is OK
- 10.1016/j.neuroimage.2006.01.021 is OK
- 10.1038/nbt.3820 is OK
- 10.1038/s41597-019-0262-8 is OK
- 10.1371/journal.pcbi.1009651 is OK
- 10.1093/cercor/bhaa288 is OK
- 10.3389/fninf.2014.00008 is OK
- 10.1016/j.neuroimage.2014.04.074 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1007/s00330-016-4485-1 is OK
- 10.1016/j.neuroimage.2019.116364 is OK
- 10.1016/j.neuroimage.2018.09.081 is OK
- 10.1097/RLI.0000000000000510 is OK
- 10.1097/RLI.0000000000000720 is OK
- 10.21105/joss.03262 is OK
- 10.1002/mrm.28825 is OK
- 10.21105/joss.02343 is OK
- 10.1002/mrm.29292 is OK
- 10.1038/s41597-022-01571-4 is OK
- 10.1002/mrm.26982 is OK
- 10.1371/journal.pone.0252966 is OK
- 10.1002/mrm.26235 is OK
- 10.1002/mrm.27421 is OK
- 10.1002/hbm.25122 is OK
- 10.1016/j.neuroimage.2015.06.040 is OK
- 10.1371/journal.pone.0189944 is OK
- 10.1016/j.ejro.2021.100357 is OK
- 10.1038/nature11971 is OK
- 10.1002/mrm.26069 is OK
- 10.1002/nbm.4564 is OK
- 10.7554/eLife.61523 is OK
- 10.1016/j.neuroimage.2009.10.002 is OK
- 10.1371/journal.pone.0069294 is OK
- 10.1111/cpf.12387 is OK
- 10.1002/jmri.25168 is OK
- 10.3389/fneur.2022.855125 is OK
- 10.1177/1352458520923970 is OK
- 10.1016/j.neuroimage.2009.01.002 is OK
- 10.1002/mrm.26058 is OK
- 10.1038/s41598-018-24304-3 is OK
- 10.1088/0031-9155/23/5/012 is OK
- 10.1002/jmri.22590 is OK
- 10.1016/j.neuroimage.2022.119488 is OK
- 10.1002/jmri.20984 is OK
- 10.1016/j.neuroimage.2022.119751 is OK
- 10.18632/aging.103629 is OK
- 10.1002/hbm.10062 is OK
- 10.1016/j.neuroimage.2004.07.051 is OK
- 10.1002/jmri.1880050111 is OK
- 10.1002/mrm.25135 is OK
- 10.1002/mrm.28779 is OK
- 10.1016/j.neuroimage.2020.116889 is OK
- 10.1016/j.neuroimage.2019.116137 is OK
- 10.1155/2014/719520 is OK
- 10.1016/j.neuroimage.2021.117910 is OK
- 10.1002/jmri.25693 is OK
- 10.1038/srep45261 is OK
- 10.1016/j.nicl.2022.103228 is OK
- 10.1109/42.906424 is OK

MISSING DOIs

- 10.3389/fnins.2020.611194 may be a valid DOI for title: Quantitative Multi-Parameter Mapping Optimized for the Clinical Routine
- 10.58530/2022/3906 may be a valid DOI for title: dMRIQCpy: A Python-Based Toolbox for Diffusion MRI Quality Control and Beyond

INVALID DOIs

- None
roboneuro commented 1 year ago

:wave: @openjournals/executable-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/neurolibre/preprints/pull/60, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

mathieuboudreau commented 1 year ago

Went through all the references and found one instance of what appears to be a mistake, MRTrix is cited for Theaud 2020 in the neurolibre version but Tournier 2019 in my manuscript draft - do I updated it in paper.md, add it to paper.bib manually, and then re-trigger roboneuro? After that, I can download and upload the updated paper.md and paper.bib files (I'm somewhat confused about this, how do those differ from the ones in my repo?)

agahkarakuzu commented 1 year ago

@mathieuboudreau you need to apply those changes in the notebook, then the new paper.md and paper.bib should contain the right citations. After you push those, I'll trigger a new extended PDF build, and if it looks good, then you can update the existing files with the ones that will be generated.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 663caffd Last updated: 2023-10-24 09:09:08 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. ℹ️ Please read and confirm the following:

    [!IMPORTANT]
    We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.

    • [ ] I, the submitting author, confirm that I have read the note above.

  5. ♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

    For the technical screener

    Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

    :warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

agahkarakuzu commented 1 year ago

@mathieuboudreau this should be fixed now, you can download paper md/bib and update them after confirming that the paper.md contains the correct citation.

image

agahkarakuzu commented 1 year ago

@roboneuro generate pdf

roboneuro 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:

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 80a4b71b Last updated: 2023-10-24 16:44:27 PDT

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on successfully crafting an open-source Neurolibre Reproducible Preprint (NRP) that navigates the cerebral maze of longitudinal stability, quantitative MRI, and myelin relaxation! This work brings scientific transparency to new heights, showcasing their neuro-expertise in a format as stable as the brain and spinal cord themselves.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

agahkarakuzu commented 1 year ago

@roboneuro production start

roboneuro commented 1 year ago

🟢 INITIATE PRODUCTION (Fork and Configure)

Status: Success 95dfb3c7 Last updated: 2023-10-24 16:45:48 PDT

:information_source: See details 
Please confirm that the forked repository is available and (_toc.yml and _config.ymlk) properly configured.
agahkarakuzu commented 1 year ago

@roboneuro production sync data

roboneuro commented 1 year ago

🟢 DATA TRANSFER (Preview --> Preprint)

Status: Success bb1ed799 Last updated: 2023-10-24 16:48:47 PDT

:information_source: See details 
Success.
agahkarakuzu commented 1 year ago

@roboneuro production build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success c8b674ec Last updated: 2023-10-24 16:55:54 PDT

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for creating the neurolibre reproducible preprint (NRP), a brainy masterpiece that combines the stability of longitudinal quantitative MRI measures with the open-source power of neurolibre, leaving no myelin sheath unturned in the quest for reproducibility!

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

agahkarakuzu commented 1 year ago

@roboneuro production sync book

roboneuro commented 1 year ago

🟢 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Success 16c61cc5 Last updated: 2023-10-24 16:56:45 PDT

:information_source: See details 
Reproducible Preprint URL (DOI formatted)
Reproducible Preprint (bare URL)
agahkarakuzu commented 1 year ago

@roboneuro zenodo create buckets

roboneuro commented 1 year ago

🟢 Reproducibility Assets - Create Zenodo buckets

Status: Success b49f5b36 Last updated: 2023-10-24 16:57:36 PDT

:information_source: See details 
Zenodo records have been created successfully: 
 {'book': {'created': '2023-10-24T23:57:18.342781+00:00', 'modified': '2023-10-24T23:57:18.626654+00:00', 'id': 10038870, 'conceptrecid': '10038869', 'metadata': {'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'publication_date': '2023-10-25', 'description': 'NeuroLibre JupyterBook built at this  reference repository/commit by roboneuro, based on the latest change by the author. 
For details, please visit the corresponding NeuroLibre technical screening.
 \n
https://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Agah Karakuzu', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-7283-271X'}, {'name': 'Arnaud Boré', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4822-1211'}, {'name': 'Basile Pinsard', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4391-3075'}, {'name': 'Kiril Zelenkovski', 'affiliation': 'Faculty of Computer Science and Engineering (FINKI), Skopje, Macedonia', 'orcid': '0000-0001-7993-7004'}, {'name': 'Eva Alonso-Ortiz', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julie Boyle', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0001-5927-221X'}, {'name': 'Pierre Bellec', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-9111-0699'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-3662-9532'}], 'contributors': [{'name': 'NeuroLibre, Admin', 'affiliation': 'NeuroLibre', 'type': 'ContactPerson'}], 'keywords': ['canadian-open-neuroscience-platform', 'neurolibre'], 'related_identifiers': [{'identifier': '10.55458/neurolibre.00018', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-by-4.0', 'imprint_publisher': 'Zenodo', 'upload_type': 'other', 'prereserve_doi': {'doi': '10.5281/zenodo.10038870', 'recid': 10038870}}, 'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10038870', 'html': 'https://zenodo.org/deposit/10038870', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10038870/files', 'bucket': 'https://zenodo.org/api/files/ab25052a-b5c0-40b8-afd5-109f9bffedaf', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10038870', 'latest_draft_html': 'https://zenodo.org/deposit/10038870', 'publish': 'https://zenodo.org/api/deposit/depositions/10038870/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10038870/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10038870/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10038870/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10038870/actions/registerconceptdoi'}, 'record_id': 10038870, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'repository': {'created': '2023-10-24T23:57:23.431668+00:00', 'modified': '2023-10-24T23:57:23.693738+00:00', 'id': 10038872, 'conceptrecid': '10038871', 'metadata': {'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'publication_date': '2023-10-25', 'description': 'GitHub archive of the  reference repository/commit by roboneuro, based on the latest change by the author. 
For details, please visit the corresponding NeuroLibre technical screening.
 \n
https://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Agah Karakuzu', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-7283-271X'}, {'name': 'Arnaud Boré', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4822-1211'}, {'name': 'Basile Pinsard', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4391-3075'}, {'name': 'Kiril Zelenkovski', 'affiliation': 'Faculty of Computer Science and Engineering (FINKI), Skopje, Macedonia', 'orcid': '0000-0001-7993-7004'}, {'name': 'Eva Alonso-Ortiz', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julie Boyle', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0001-5927-221X'}, {'name': 'Pierre Bellec', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-9111-0699'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-3662-9532'}], 'contributors': [{'name': 'NeuroLibre, Admin', 'affiliation': 'NeuroLibre', 'type': 'ContactPerson'}], 'keywords': ['canadian-open-neuroscience-platform', 'neurolibre'], 'related_identifiers': [{'identifier': '10.55458/neurolibre.00018', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-by-4.0', 'imprint_publisher': 'Zenodo', 'upload_type': 'software', 'prereserve_doi': {'doi': '10.5281/zenodo.10038872', 'recid': 10038872}}, 'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10038872', 'html': 'https://zenodo.org/deposit/10038872', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10038872/files', 'bucket': 'https://zenodo.org/api/files/e6a3dcb7-f999-4123-b16e-211aed59275e', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10038872', 'latest_draft_html': 'https://zenodo.org/deposit/10038872', 'publish': 'https://zenodo.org/api/deposit/depositions/10038872/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10038872/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10038872/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10038872/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10038872/actions/registerconceptdoi'}, 'record_id': 10038872, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'data': {'created': '2023-10-24T23:57:28.496118+00:00', 'modified': '2023-10-24T23:57:28.775919+00:00', 'id': 10038874, 'conceptrecid': '10038873', 'metadata': {'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'publication_date': '2023-10-25', 'description': 'Dataset provided for NeuroLibre preprint.\n Author repo: https://github.com/courtois-neuromod/anat-processing-paper \nNeuroLibre fork:https://github.com/roboneurolibre/anat-processing-paper 
For details, please visit the corresponding NeuroLibre technical screening.
  \n
https://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Agah Karakuzu', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-7283-271X'}, {'name': 'Arnaud Boré', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4822-1211'}, {'name': 'Basile Pinsard', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4391-3075'}, {'name': 'Kiril Zelenkovski', 'affiliation': 'Faculty of Computer Science and Engineering (FINKI), Skopje, Macedonia', 'orcid': '0000-0001-7993-7004'}, {'name': 'Eva Alonso-Ortiz', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julie Boyle', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0001-5927-221X'}, {'name': 'Pierre Bellec', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-9111-0699'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-3662-9532'}], 'contributors': [{'name': 'NeuroLibre, Admin', 'affiliation': 'NeuroLibre', 'type': 'ContactPerson'}], 'keywords': ['canadian-open-neuroscience-platform', 'neurolibre'], 'related_identifiers': [{'identifier': '10.55458/neurolibre.00018', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-zero', 'imprint_publisher': 'Zenodo', 'upload_type': 'dataset', 'prereserve_doi': {'doi': '10.5281/zenodo.10038874', 'recid': 10038874}}, 'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10038874', 'html': 'https://zenodo.org/deposit/10038874', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10038874/files', 'bucket': 'https://zenodo.org/api/files/921218ea-225e-49ec-90bf-0c04ed3c183c', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10038874', 'latest_draft_html': 'https://zenodo.org/deposit/10038874', 'publish': 'https://zenodo.org/api/deposit/depositions/10038874/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10038874/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10038874/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10038874/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10038874/actions/registerconceptdoi'}, 'record_id': 10038874, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'docker': {'created': '2023-10-24T23:57:33.575671+00:00', 'modified': '2023-10-24T23:57:33.863530+00:00', 'id': 10038876, 'conceptrecid': '10038875', 'metadata': {'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'publication_date': '2023-10-25', 'description': 'Docker image built from the  reference repository/commit by roboneuro, based on the latest change by the author, using repo2docker (through BinderHub). 
 To run locally: 
     
  1. docker load < DockerImage_10.55458_NeuroLibre_00018_eb3427.tar.gz
  2. docker run -it --rm -p 8888:8888 DOCKER_IMAGE_ID jupyter lab --ip 0.0.0.0
     
 
by replacing DOCKER_IMAGE_ID above with the respective ID of the Docker image loaded from the zip file.
 
For details, please visit the corresponding NeuroLibre technical screening.
 \n
https://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Agah Karakuzu', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-7283-271X'}, {'name': 'Arnaud Boré', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4822-1211'}, {'name': 'Basile Pinsard', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-4391-3075'}, {'name': 'Kiril Zelenkovski', 'affiliation': 'Faculty of Computer Science and Engineering (FINKI), Skopje, Macedonia', 'orcid': '0000-0001-7993-7004'}, {'name': 'Eva Alonso-Ortiz', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julie Boyle', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0001-5927-221X'}, {'name': 'Pierre Bellec', 'affiliation': "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, QC, Canada", 'orcid': '0000-0002-9111-0699'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-3662-9532'}], 'contributors': [{'name': 'NeuroLibre, Admin', 'affiliation': 'NeuroLibre', 'type': 'ContactPerson'}], 'keywords': ['canadian-open-neuroscience-platform', 'neurolibre'], 'related_identifiers': [{'identifier': '10.55458/neurolibre.00018', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-by-4.0', 'imprint_publisher': 'Zenodo', 'upload_type': 'software', 'prereserve_doi': {'doi': '10.5281/zenodo.10038876', 'recid': 10038876}}, 'title': 'Longitudinal stability of brain and spinal cord quantitative MRI measures', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10038876', 'html': 'https://zenodo.org/deposit/10038876', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10038876/files', 'bucket': 'https://zenodo.org/api/files/432c4c6d-723a-4abc-a982-b996a33e01e0', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10038876', 'latest_draft_html': 'https://zenodo.org/deposit/10038876', 'publish': 'https://zenodo.org/api/deposit/depositions/10038876/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10038876/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10038876/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10038876/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10038876/actions/registerconceptdoi'}, 'record_id': 10038876, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}}
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload book
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🔴  Reproducibility Assets - Archive Jupyter Book 




Status: Failed f0762c9f
Last updated: 2023-10-24 16:58:28 PDT 


 :information_source: See details 
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload book
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🔴  Reproducibility Assets - Archive Jupyter Book 




Status: Failed c3516387
Last updated: 2023-10-24 17:40:50 PDT 


 :information_source: See details 
{"status": 403, "message": "Permission denied."}
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro production upload book
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

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


@roboneuro commands
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload book
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🔴  Reproducibility Assets - Archive Jupyter Book 




Status: Failed e00b13c9
Last updated: 2023-10-24 20:06:35 PDT 


 :information_source: See details 
{"status": 403, "message": "Permission denied."}
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload book
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🔴  Reproducibility Assets - Archive Jupyter Book 




Status: Failed f0fda981
Last updated: 2023-10-25 07:22:59 PDT 


 :information_source: See details 
{"status": 403, "message": "Permission denied."}
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload book
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🟢  Reproducibility Assets - Archive Jupyter Book 




Status: Success 2b35d3b9
Last updated: 2023-10-25 08:07:49 PDT 


 :information_source: See details 
Successful /DATA/zenodo/00018/JupyterBook_10.55458_NeuroLibre_00018_eb3427 to https://zenodo.org/api/files/ab25052a-b5c0-40b8-afd5-109f9bffedaf
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload repository
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🔴  Reproducibility Assets - Archive GitHub Repository 




Status: Failed 652119ae
Last updated: 2023-10-25 08:08:32 PDT 


 :information_source: See details 
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload docker
            

        

            

            

                roboneuro
                commented
                 1 year ago            

            

                
🟢  Reproducibility Assets - Archive Docker Image 




Status: Success 053061d4
Last updated: 2023-10-25 08:14:05 PDT 


 :information_source: See details 
Successful /DATA/zenodo/00018/DockerImage_10.55458_NeuroLibre_00018_eb3427.tar.gz to https://zenodo.org/api/files/432c4c6d-723a-4abc-a982-b996a33e01e0
            

        

            

            

                agahkarakuzu
                commented
                 1 year ago            

            

                
@roboneuro zenodo upload repository