[REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"

roboneuro commented 9 months ago

Submitting author: !--author-handle-->@mathieuboudreau@pbellec@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00025 Repository archive: 10.5281/zenodo.10844540 Data archive: 10.5281/zenodo.10844542 Book archive: 10.5281/zenodo.10844538 Docker archive: 10.5281/zenodo.10844544

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a"><img src="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg)](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a)

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 @pbellec 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 8 months ago

@roboneuro zenodo flush

roboneuro commented 8 months ago

🟢 ZENODO FLUSH RECORDS AND UPLOADS

Status: Success 3ae0a1d9 Last updated: 2024-03-20 05:27:23 PDT

:information_source: See details


 Deleted book deposit successfully.
 [] did not exist.[] did not exist.
 Deleted repository deposit successfully.
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 Deleted data deposit successfully.
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 Deleted old deposit records from the server: /DATA/zenodo_records/00025/zenodo_deposit_NeuroLibre_00025.json

agahkarakuzu commented 8 months ago

@roboneuro zenodo create buckets

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Create Zenodo buckets

Status: Success 109ed600 Last updated: 2024-03-20 05:33:12 PDT

:information_source: See details

Zenodo records have been created successfully: 
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 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10843811', 'recid': 10843811}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10843811', 'html': 'https://zenodo.org/deposit/10843811', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10843811/files', 'bucket': 'https://zenodo.org/api/files/06e644f0-c41f-4fd3-a908-0a3633086045', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10843811', 'latest_draft_html': 'https://zenodo.org/deposit/10843811', 'publish': 'https://zenodo.org/api/deposit/depositions/10843811/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10843811/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10843811/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10843811/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10843811/actions/registerconceptdoi'}, 'record_id': 10843811, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'repository': {'created': '2024-03-20T12:32:59.334718+00:00', 'modified': '2024-03-20T12:32:59.616419+00:00', 'id': 10843813, 'conceptrecid': '10843812', 'metadata': {'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10843813', 'recid': 10843813}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10843813', 'html': 'https://zenodo.org/deposit/10843813', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10843813/files', 'bucket': 'https://zenodo.org/api/files/ef3f4dd1-145b-481f-bf04-4312173bafbb', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10843813', 'latest_draft_html': 'https://zenodo.org/deposit/10843813', 'publish': 'https://zenodo.org/api/deposit/depositions/10843813/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10843813/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10843813/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10843813/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10843813/actions/registerconceptdoi'}, 'record_id': 10843813, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'data': {'created': '2024-03-20T12:33:05.165505+00:00', 'modified': '2024-03-20T12:33:05.300473+00:00', 'id': 10843815, 'conceptrecid': '10843814', 'metadata': {'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', 'description': 'Dataset provided for NeuroLibre preprint.\n Author repo: https://github.com/shimming-toolbox/rf-shimming-7t \nNeuroLibre fork:https://github.com/roboneurolibre/rf-shimming-7t For details, please visit the corresponding NeuroLibre technical screening.
  \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-zero', 'imprint_publisher': 'Zenodo', 'upload_type': 'dataset', 'prereserve_doi': {'doi': '10.5281/zenodo.10843815', 'recid': 10843815}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10843815', 'html': 'https://zenodo.org/deposit/10843815', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10843815/files', 'bucket': 'https://zenodo.org/api/files/11cb67b1-08e8-46a3-b115-8e86b6fc256c', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10843815', 'latest_draft_html': 'https://zenodo.org/deposit/10843815', 'publish': 'https://zenodo.org/api/deposit/depositions/10843815/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10843815/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10843815/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10843815/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10843815/actions/registerconceptdoi'}, 'record_id': 10843815, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'docker': {'created': '2024-03-20T12:33:10.626567+00:00', 'modified': '2024-03-20T12:33:10.731936+00:00', 'id': 10843817, 'conceptrecid': '10843816', 'metadata': {'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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:  docker load < DockerImage_10.55458_NeuroLibre_00025_6a2af5.tar.gz
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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10843817', 'recid': 10843817}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10843817', 'html': 'https://zenodo.org/deposit/10843817', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10843817/files', 'bucket': 'https://zenodo.org/api/files/6ed7bdcf-7dfb-4232-9dc2-6cd155e5d21a', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10843817', 'latest_draft_html': 'https://zenodo.org/deposit/10843817', 'publish': 'https://zenodo.org/api/deposit/depositions/10843817/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10843817/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10843817/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10843817/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10843817/actions/registerconceptdoi'}, 'record_id': 10843817, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}}

agahkarakuzu commented 8 months ago

@roboneuro zenodo flush

roboneuro commented 8 months ago

🟢 ZENODO FLUSH RECORDS AND UPLOADS

Status: Success 6cd79257 Last updated: 2024-03-20 07:19:29 PDT

:information_source: See details


 Deleted book deposit successfully.
 [] did not exist.[] did not exist.
 Deleted repository deposit successfully.
 [] did not exist.[] did not exist.
 Deleted data deposit successfully.
 [] did not exist.[] did not exist.
 Deleted docker deposit successfully.
 [] did not exist.[] did not exist.
 Deleted old deposit records from the server: /DATA/zenodo_records/00025/zenodo_deposit_NeuroLibre_00025.json

agahkarakuzu commented 8 months ago

@roboneuro zenodo create buckets

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Create Zenodo buckets

Status: Success 49f30a74 Last updated: 2024-03-20 07:20:20 PDT

:information_source: See details

Zenodo records have been created successfully: 
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 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10844483', 'recid': 10844483}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844483', 'html': 'https://zenodo.org/deposit/10844483', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844483/files', 'bucket': 'https://zenodo.org/api/files/ba31140f-25e8-4788-99a6-19f9d80009a7', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844483', 'latest_draft_html': 'https://zenodo.org/deposit/10844483', 'publish': 'https://zenodo.org/api/deposit/depositions/10844483/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844483/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844483/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844483/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844483/actions/registerconceptdoi'}, 'record_id': 10844483, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'repository': {'created': '2024-03-20T14:20:06.539758+00:00', 'modified': '2024-03-20T14:20:06.625996+00:00', 'id': 10844489, 'conceptrecid': '10844488', 'metadata': {'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10844489', 'recid': 10844489}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844489', 'html': 'https://zenodo.org/deposit/10844489', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844489/files', 'bucket': 'https://zenodo.org/api/files/9842b328-511d-4a08-9fd7-7a23b249cd91', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844489', 'latest_draft_html': 'https://zenodo.org/deposit/10844489', 'publish': 'https://zenodo.org/api/deposit/depositions/10844489/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844489/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844489/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844489/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844489/actions/registerconceptdoi'}, 'record_id': 10844489, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'data': {'created': '2024-03-20T14:20:12.212372+00:00', 'modified': '2024-03-20T14:20:12.302552+00:00', 'id': 10844491, 'conceptrecid': '10844490', 'metadata': {'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', 'description': 'Dataset provided for NeuroLibre preprint.\n Author repo: https://github.com/shimming-toolbox/rf-shimming-7t \nNeuroLibre fork:https://github.com/roboneurolibre/rf-shimming-7t For details, please visit the corresponding NeuroLibre technical screening.
  \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-zero', 'imprint_publisher': 'Zenodo', 'upload_type': 'dataset', 'prereserve_doi': {'doi': '10.5281/zenodo.10844491', 'recid': 10844491}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844491', 'html': 'https://zenodo.org/deposit/10844491', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844491/files', 'bucket': 'https://zenodo.org/api/files/876795f8-df8e-484d-b59f-be940e52ada0', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844491', 'latest_draft_html': 'https://zenodo.org/deposit/10844491', 'publish': 'https://zenodo.org/api/deposit/depositions/10844491/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844491/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844491/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844491/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844491/actions/registerconceptdoi'}, 'record_id': 10844491, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'docker': {'created': '2024-03-20T14:20:17.701131+00:00', 'modified': '2024-03-20T14:20:17.875369+00:00', 'id': 10844493, 'conceptrecid': '10844492', 'metadata': {'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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:  docker load < DockerImage_10.55458_NeuroLibre_00025_6a2af5.tar.gz
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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10844493', 'recid': 10844493}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844493', 'html': 'https://zenodo.org/deposit/10844493', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844493/files', 'bucket': 'https://zenodo.org/api/files/ab82cde2-c10d-4fe3-9d44-86c73764f5e1', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844493', 'latest_draft_html': 'https://zenodo.org/deposit/10844493', 'publish': 'https://zenodo.org/api/deposit/depositions/10844493/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844493/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844493/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844493/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844493/actions/registerconceptdoi'}, 'record_id': 10844493, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}}

agahkarakuzu commented 8 months ago

@roboneuro zenodo flush

roboneuro commented 8 months ago

🟢 ZENODO FLUSH RECORDS AND UPLOADS

Status: Success d6afd74b Last updated: 2024-03-20 07:29:22 PDT

:information_source: See details


 Deleted book deposit successfully.
 [] did not exist.[] did not exist.
 Deleted repository deposit successfully.
 [] did not exist.[] did not exist.
 Deleted data deposit successfully.
 [] did not exist.[] did not exist.
 Deleted docker deposit successfully.
 [] did not exist.[] did not exist.
 Deleted old deposit records from the server: /DATA/zenodo_records/00025/zenodo_deposit_NeuroLibre_00025.json

agahkarakuzu commented 8 months ago

@roboneuro zenodo create buckets

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Create Zenodo buckets

Status: Success 2b9722ce Last updated: 2024-03-20 07:33:19 PDT

:information_source: See details

Zenodo records have been created successfully: 
 {'book': {'created': '2024-03-20T14:33:01.280134+00:00', 'modified': '2024-03-20T14:33:01.356210+00:00', 'id': 10844538, 'conceptrecid': '10844537', 'metadata': {'title': '(JupyterBook) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10844538', 'recid': 10844538}}, 'title': '(JupyterBook) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844538', 'html': 'https://zenodo.org/deposit/10844538', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844538/files', 'bucket': 'https://zenodo.org/api/files/197daa24-aa7f-425c-9cc6-3567c23b085b', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844538', 'latest_draft_html': 'https://zenodo.org/deposit/10844538', 'publish': 'https://zenodo.org/api/deposit/depositions/10844538/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844538/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844538/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844538/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844538/actions/registerconceptdoi'}, 'record_id': 10844538, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'repository': {'created': '2024-03-20T14:33:06.787846+00:00', 'modified': '2024-03-20T14:33:06.863017+00:00', 'id': 10844540, 'conceptrecid': '10844539', 'metadata': {'title': '(GitHubRepo) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10844540', 'recid': 10844540}}, 'title': '(GitHubRepo) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844540', 'html': 'https://zenodo.org/deposit/10844540', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844540/files', 'bucket': 'https://zenodo.org/api/files/12e8d9de-2e34-46c4-a6dc-ff29775ceb37', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844540', 'latest_draft_html': 'https://zenodo.org/deposit/10844540', 'publish': 'https://zenodo.org/api/deposit/depositions/10844540/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844540/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844540/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844540/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844540/actions/registerconceptdoi'}, 'record_id': 10844540, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'data': {'created': '2024-03-20T14:33:12.122385+00:00', 'modified': '2024-03-20T14:33:12.180355+00:00', 'id': 10844542, 'conceptrecid': '10844541', 'metadata': {'title': '(Dataset) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', 'description': 'Dataset provided for NeuroLibre preprint.\n Author repo: https://github.com/shimming-toolbox/rf-shimming-7t \nNeuroLibre fork:https://github.com/roboneurolibre/rf-shimming-7t For details, please visit the corresponding NeuroLibre technical screening.
  \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', 'relation': 'isPartOf', 'resource_type': 'publication-preprint', 'scheme': 'doi'}], 'license': 'cc-zero', 'imprint_publisher': 'Zenodo', 'upload_type': 'dataset', 'prereserve_doi': {'doi': '10.5281/zenodo.10844542', 'recid': 10844542}}, 'title': '(Dataset) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844542', 'html': 'https://zenodo.org/deposit/10844542', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844542/files', 'bucket': 'https://zenodo.org/api/files/bd48c4a8-759f-42ce-a67a-72f2c8c752a3', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844542', 'latest_draft_html': 'https://zenodo.org/deposit/10844542', 'publish': 'https://zenodo.org/api/deposit/depositions/10844542/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844542/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844542/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844542/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844542/actions/registerconceptdoi'}, 'record_id': 10844542, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'docker': {'created': '2024-03-20T14:33:17.607691+00:00', 'modified': '2024-03-20T14:33:17.687972+00:00', 'id': 10844544, 'conceptrecid': '10844543', 'metadata': {'title': '(DockerImage) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'publication_date': '2024-03-20', '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:  docker load < DockerImage_10.55458_NeuroLibre_00025_6a2af5.tar.gz
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.
 \nhttps://neurolibre.org
', 'access_right': 'open', 'creators': [{'name': 'Daniel Papp', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-1481-1413'}, {'name': 'Kyle M. Gilbert', 'affiliation': 'Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada', 'orcid': '0000-0003-3026-5686'}, {'name': 'Gaspard Cereza', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada'}, {'name': "Alexandre D'Astous", 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0003-0381-7334'}, {'name': 'Nibardo Lopez-Rios', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-4791-8260'}, {'name': 'Mathieu Boudreau', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0002-7726-4456'}, {'name': 'Marcus Couch', 'affiliation': 'Siemens Healthcare Limited, Montreal, QC, Canada', 'orcid': '0000-0002-2732-8941'}, {'name': 'Pedram Yazdanbakhsh', 'affiliation': 'McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada', 'orcid': '0000-0003-4456-5997'}, {'name': 'Robert L. Barry', 'affiliation': 'Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA'}, {'name': 'Eva Alonso Ortiz', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada', 'orcid': '0000-0001-6590-7234'}, {'name': 'Julien Cohen-Adad', 'affiliation': 'NeuroPoly Lab, Institute of Biomedical Engineering, 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.00025', '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.10844544', 'recid': 10844544}}, 'title': '(DockerImage) Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10844544', 'html': 'https://zenodo.org/deposit/10844544', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10844544/files', 'bucket': 'https://zenodo.org/api/files/b3b749c5-55a5-4934-9404-3498af695534', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10844544', 'latest_draft_html': 'https://zenodo.org/deposit/10844544', 'publish': 'https://zenodo.org/api/deposit/depositions/10844544/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10844544/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10844544/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10844544/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10844544/actions/registerconceptdoi'}, 'record_id': 10844544, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}}

agahkarakuzu commented 8 months ago

@roboneuro zenodo upload book

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Archive Jupyter Book

Status: Success 8e881485 Last updated: 2024-03-20 07:35:49 PDT

:information_source: See details

Successful /DATA/zenodo/00025/JupyterBook_10.55458_NeuroLibre_00025_6a2af5.zip to https://zenodo.org/api/files/197daa24-aa7f-425c-9cc6-3567c23b085b

agahkarakuzu commented 8 months ago

@roboneuro zenodo upload data

roboneuro commented 8 months ago

🔴 Reproducibility Assets - Archive Data

Status: Failed b5f52daa Last updated: 2024-03-20 07:39:27 PDT

:information_source: See details

An exception has occurred: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))

agahkarakuzu commented 8 months ago

@roboneuro zenodo upload repository

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Archive GitHub Repository

Status: Success 228c434a Last updated: 2024-03-20 07:37:10 PDT

:information_source: See details

Successful /DATA/zenodo/00025/GitHubRepo_10.55458_NeuroLibre_00025_6a2af5.zip to https://zenodo.org/api/files/12e8d9de-2e34-46c4-a6dc-ff29775ceb37

agahkarakuzu commented 8 months ago

@roboneuro zenodo upload docker

roboneuro commented 8 months ago

🔴 Reproducibility Assets - Archive Docker Image

Status: Failed 6fb5779f Last updated: 2024-03-20 07:58:12 PDT

:information_source: See details

An exception has occurred: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))

agahkarakuzu commented 8 months ago

@roboneuro zenodo status

roboneuro commented 8 months ago

Deposit

:green_square: Zenodo deposit records are found.

Upload

:green_circle: Repository archive
- 3.04 MB zenodo_uploaded_repository_NeuroLibre_00025_6a2af5.json
:red_circle: Data archive is missing
:green_circle: Book archive
- 4.59 MB zenodo_uploaded_book_NeuroLibre_00025_6a2af5.json
:red_circle: Docker archive is missing

Publish

:small_red_triangle_down: Zenodo DOIs have not been published yet.

agahkarakuzu commented 8 months ago

@roboneuro zenodo upload data

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Archive Data

Status: Success f50b0035 Last updated: 2024-03-20 18:02:38 PDT

:information_source: See details

Successful /DATA/zenodo/00025/Dataset_10.55458_NeuroLibre_00025_6a2af5.zip to https://zenodo.org/api/files/bd48c4a8-759f-42ce-a67a-72f2c8c752a3

agahkarakuzu commented 8 months ago

@roboneuro zenodo upload docker

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Archive Docker Image

Status: Success 1318f69b Last updated: 2024-03-20 18:06:34 PDT

:information_source: See details

Successful /DATA/zenodo/00025/DockerImage_10.55458_NeuroLibre_00025_6a2af5.tar.gz to https://zenodo.org/api/files/b3b749c5-55a5-4934-9404-3498af695534

agahkarakuzu commented 8 months ago

@roboneuro zenodo status

roboneuro commented 8 months ago

Deposit

:green_square: Zenodo deposit records are found.

Upload

:green_circle: Repository archive
- 3.04 MB zenodo_uploaded_repository_NeuroLibre_00025_6a2af5.json
:green_circle: Data archive
- 1.74 GB zenodo_uploaded_data_NeuroLibre_00025_6a2af5.json
:green_circle: Book archive
- 4.59 MB zenodo_uploaded_book_NeuroLibre_00025_6a2af5.json
:green_circle: Docker archive
- 2.98 GB zenodo_uploaded_docker_NeuroLibre_00025_6a2af5.json

Publish

:small_red_triangle_down: Zenodo DOIs have not been published yet.

agahkarakuzu commented 8 months ago

@roboneuro generate pdf

roboneuro commented 8 months ago

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

agahkarakuzu commented 8 months ago

@roboneuro recommend-accept

roboneuro commented 8 months ago

Attempting dry run of processing paper acceptance...

roboneuro commented 8 months ago

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

OK DOIs

- 10.1002/mrm.29528 is OK
- 10.1016/j.neuroimage.2016.10.009 is OK
- 10.1038/nrneurol.2015.80 is OK
- 10.1038/s41582-019-0270-5 is OK
- 10.1016/S0730-725X(01)00300-9 is OK
- 10.1002/jmri.20245 is OK
- 10.1118/1.595995 is OK
- 10.1002/mrm.10137 is OK
- 10.1016/j.neuroimage.2017.10.041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

roboneuro commented 8 months ago

:wave: @neurolibre/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/77, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

agahkarakuzu commented 8 months ago

@roboneuro zenodo publish

roboneuro commented 8 months ago

🟠 Publish Reproducibility Assets

Status: In progress d2441434 Last updated: 2024-03-29 00:32:24 PDT

:information_source: See details

Let's freeze those reproducibility assets in time! Publishing the Zenodo records.

:recycle: Refresh

agahkarakuzu commented 8 months ago

@roboneuro zenodo publish

roboneuro commented 8 months ago

🟠 Publish Reproducibility Assets

Status: In progress fe3f2f14 Last updated: 2024-03-29 01:52:44 PDT

:information_source: See details

As the reproducibility assets have already been published, I will just set the DOIs.

:recycle: Refresh

agahkarakuzu commented 8 months ago

@roboneuro zenodo publish

roboneuro commented 8 months ago

🟠 Publish Reproducibility Assets

Status: In progress f7cde9a4 Last updated: 2024-03-29 07:43:07 PDT

:information_source: See details

As the reproducibility assets have already been published, I will just set the DOIs.

:recycle: Refresh

agahkarakuzu commented 8 months ago

@roboneuro zenodo publish

roboneuro commented 8 months ago

🟠 Publish Reproducibility Assets

Status: In progress 5b3258fc Last updated: 2024-04-02 08:54:03 PDT

:information_source: See details

As the reproducibility assets have already been published, I will just set the DOIs.

:recycle: Refresh

agahkarakuzu commented 8 months ago

@roboneuro zenodo publish

agahkarakuzu commented 8 months ago

@roboneuro zenodo publish

roboneuro commented 8 months ago

🟣 Publish Reproducibility Assets

Status: Already exists 2e6c5dc0 Last updated: 2024-04-04 13:11:57 PDT

Looks like the reproducibility assets have already been published! So...

GPT is AFK, keep hanging out with roboneuro.

roboneuro commented 8 months ago

@roboneuro set 10.5281/zenodo.10844538 as book archive

roboneuro commented 8 months ago

@roboneuro set 10.5281/zenodo.10844540 as repository archive

roboneuro commented 8 months ago

@roboneuro set 10.5281/zenodo.10844542 as data archive

roboneuro commented 8 months ago

@roboneuro set 10.5281/zenodo.10844544 as docker archive

agahkarakuzu commented 8 months ago

@roboneuro set 10.5281/zenodo.10844538 as book archive

neurolibre / neurolibre-reviews