[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

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Markdown: [![status](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg)](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a)

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roboneuro commented 9 months ago

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

mathieuboudreau commented 9 months ago

@roboneuro generate pdf

roboneuro commented 9 months ago

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

mathieuboudreau commented 9 months ago

@agahkarakuzu is there a way to set the size of the figures in paper.md? Fig 3 is going into the footnote area:

agahkarakuzu commented 9 months ago

@mathieuboudreau

Figure sizes can be customized by adding an optional second parameter:
![Caption for example figure.](figure.png){ width=20% }

Anything here applies.

mathieuboudreau commented 9 months ago

@roboneuro generate pdf

roboneuro commented 9 months ago

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

mathieuboudreau commented 9 months ago

@roboneuro generate pdf

roboneuro commented 9 months ago

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

mathieuboudreau commented 9 months ago

@roboneuro generate pdf

roboneuro commented 9 months ago

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

mathieuboudreau commented 9 months ago

@agahkarakuzu following our discussion late last week, here are several updates:

I did a rudimentary attempt of running the notebook in NeuroLibre by copying the data from the servers into the container, and 1) it was quite quick (can't recall, 10-15 secconds maybe?), an 2) running SCT by giving this copied folder didn't raise any errors due to write permissions. I think this is the best way forward to ensure the "clean" mode runs (which in its current state, it wouldn't on NeuroLibre due to the mistake introduced in your changes about the expected output locations / saved output locations to cicrcumvent NeuroLibre's read-only data folder), and it will simplify compatibility with running it in Colab (which it didn't due to the changes introduced that I just mentioned).
As expected, running the analysis code failed on the test servers with the changes above, due to insufficient RAM on the test server (6GB).
Although you said you din't think it would work, I attempted opening a NeuroLibre session on the production servers via my T1 manuscript link, and then attempted to install SCT and the rf-shimming repo's pip dependencies, and had no issue. The only main issue was I couln't in that environment figure out how to let the Notebook cell's bash cells see SCT in it's path (I tried nearly everything), so had to circumvent that by hardcoding the paths of the SCT calls.
Following the above, I was able to run a "clean" version of the notebook (i.e. full pipeline with just the raw data) on the production servers to test if the extra ram (8GB) was going to be sufficient.
On initial tests, it seemed to get quite close to the limit (I think I saw up to like 7.8GB / 8GB), but didn't crash during the registration step of the pipeline.
I ran it on the weekend overnight, here's some information about it:

1) It took just under 6 hours to complete on NeuroLibre:

vs the ~2 hours on Google Colab. So NeuroLibre was about 3x slower to process this notebook than Colab, but I'm still relieved it was able to do it!

2) I'll have to check but I felt the B1 registration step went much quicker than the Colab runs, but maybe I just never looked closely. Just writing this so I remember to check that there wasn't a left-over processed file that wasn't deleted during the cleanup adfter copying from the NeuroLibre servers that would have sped up the processing.

3) The anat/T2starw stats table reproduced exactly the Google Colab table:

NeuroLibre container (left) / Colab table (in jupyter book) (right)

4) As for the B1 table, the stats table produced by NeuroLibre differed slightly starting at the 3rd significant digit.

I don't know enough about the pipeline/SCT to speculate why, besides maybe slight difference in preprocessing the B1 data in the pipeline due to a different pip version of a dependency installed by pip between the two, or due to a difference in floating point values between hardwares. I'm going to double check point no. 2 above also

I'll consolidate the changes described above in a notebook & make it colab/repo2docker compatible, and will make a PR for it in the rf-shimming repo.

jcohenadad commented 9 months ago

i'm wondering if the difference comes from SCT or from the statistical library (different version, different hardware). This could be verified by comparing the CSV files (if they are the same, then it's the stats lib)

mathieuboudreau commented 9 months ago

i'm wondering if the difference comes from SCT or from the statistical library (different version, different hardware). This could be verified by comparing the CSV files (if they are the same, then it's the stats lib)

Thanks for this idea - I just did that, and found no differences in CSV files generated on NeuroLibre vs Colab (up to the 15 digits stored in the CSVs), and both environments are running version 0.14.1 of the statsmodel package. So I it's still possible source of this difference might be the hardware numerical precision when the stats model is called (maybe when the values are loaded & stored), or there's a dependency that statsmodel is using that's not the same version on both environment.

agahkarakuzu commented 8 months ago

@roboneuro build book

roboneuro commented 8 months ago

🟢 Successfully built

Status: Success b1c9c805 Last updated: 2024-03-07 03:49:15 PST

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 8 months ago

:confetti_ball::confetti_ball::confetti_ball: Good news!

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

agahkarakuzu commented 8 months ago

@mathieuboudreau @jcohenadad if you are happy with this latest build above, I'll start the production workflow.

jcohenadad commented 8 months ago

go for it :-) thanks!

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

@mathieuboudreau another question:

Are these identical? If so, I will set the existing openneuro DOI for the data.

mathieuboudreau commented 8 months ago

@mathieuboudreau another question:

10.18112/openneuro.ds004906.v2.4.0

https://github.com/shimming-toolbox/rf-shimming-7t/releases/download/r20240214/ds004906.zip

Are these identical? If so, I will set the existing openneuro DOI for the data.

Not identical; open neuro has only the raw data while the release has raw + processed (for quicker/easier plotting in NeuroLibre)

agahkarakuzu commented 8 months ago

Alright, thanks! There are small issues with citations on the paper.md, I have fixed them locally, will push it after production as the last step.

agahkarakuzu commented 8 months ago

@roboneuro production sync data

roboneuro commented 8 months ago

🟢 DATA TRANSFER (Preview --> Preprint)

Status: Success 1bd4f4c9 Last updated: 2024-03-18 19:29:29 PDT

:information_source: See details

Success.

agahkarakuzu commented 8 months ago

@roboneuro production start

roboneuro commented 8 months ago

🟢 INITIATE PRODUCTION (Fork and Configure)

Status: Success 0f9452e9 Last updated: 2024-03-18 19:34:33 PDT

:information_source: See details

Please confirm that the forked repository is available and (_toc.yml and _config.ymlk) properly configured.

agahkarakuzu commented 8 months ago

@roboneuro production build book

roboneuro commented 8 months ago

🔴 Binder build has failed 🥀

Status: Failed b530790c Last updated: 2024-03-18 19:37:52 PDT

:information_source: See details

The next comment will forward the logs

roboneuro commented 8 months ago

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for roboneurolibre/rf-shimming-7t at 814c1067ba1184a4abb83d5b39746d94dc13a902

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu commented 8 months ago

@roboneuro production start

roboneuro commented 8 months ago

🟢 INITIATE PRODUCTION (Fork and Configure)

Status: Success 639c9488 Last updated: 2024-03-19 06:22:55 PDT

:information_source: See details

Please confirm that the forked repository is available and (_toc.yml and _config.ymlk) properly configured.

agahkarakuzu commented 8 months ago

@roboneuro production build book

agahkarakuzu commented 8 months ago

@roboneuro production build book

roboneuro commented 8 months ago

🟢 Successfully built

Status: Success 7249ef63 Last updated: 2024-03-19 18:56:37 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 8 months ago

:confetti_ball::confetti_ball::confetti_ball: Good news!

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

agahkarakuzu commented 8 months ago

@roboneuro production sync book

roboneuro commented 8 months ago

🟢 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Success bf9ae27b Last updated: 2024-03-19 18:59:25 PDT

:information_source: See details

Reproducible Preprint URL (DOI formatted)Reproducible Preprint (bare URL)

agahkarakuzu commented 8 months ago

@roboneuro commands

roboneuro commented 8 months ago

Hello @agahkarakuzu, here are the things you can ask me to do:


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@roboneuro remind @reviewer in 2 weeks

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@roboneuro check references

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@roboneuro check repository

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@roboneuro generate my checklist

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@roboneuro set v1.0.0 as version

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@roboneuro set https://github.com/organization/repo as repository

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@roboneuro set set 10.5281/zenodo.6861996 as archive

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@roboneuro set 10.5281/zenodo.6861996 as data archive

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agahkarakuzu commented 8 months ago

@roboneuro set book uri

roboneuro commented 8 months ago

Done, set the URI for the reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00025

roboneuro commented 8 months ago

:page_with_curl: Looks like the summary PDF is not available on the NeuroLibre servers yet.

agahkarakuzu commented 8 months ago

@roboneuro zenodo create buckets

roboneuro commented 8 months ago

🟢 Reproducibility Assets - Create Zenodo buckets

Status: Success 1b83ad10 Last updated: 2024-03-19 19:49:08 PDT

:information_source: See details

Zenodo records have been created successfully: 
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 \nhttps://neurolibre.org
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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': 'software', 'prereserve_doi': {'doi': '10.5281/zenodo.10841701', 'recid': 10841701}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841701', 'html': 'https://zenodo.org/deposit/10841701', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841701/files', 'bucket': 'https://zenodo.org/api/files/90f530e4-2a9b-4e4b-9ae7-cc1c8964ec5b', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841701', 'latest_draft_html': 'https://zenodo.org/deposit/10841701', 'publish': 'https://zenodo.org/api/deposit/depositions/10841701/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841701/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841701/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841701/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841701/actions/registerconceptdoi'}, 'record_id': 10841701, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'data': {'created': '2024-03-20T02:49:00.370163+00:00', 'modified': '2024-03-20T02:49:00.448770+00:00', 'id': 10841703, 'conceptrecid': '10841702', '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.10841703', 'recid': 10841703}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841703', 'html': 'https://zenodo.org/deposit/10841703', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841703/files', 'bucket': 'https://zenodo.org/api/files/e43497ec-4f90-4af8-a409-db809f6bce1e', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841703', 'latest_draft_html': 'https://zenodo.org/deposit/10841703', 'publish': 'https://zenodo.org/api/deposit/depositions/10841703/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841703/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841703/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841703/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841703/actions/registerconceptdoi'}, 'record_id': 10841703, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'docker': {'created': '2024-03-20T02:49:05.927586+00:00', 'modified': '2024-03-20T02:49:06.024782+00:00', 'id': 10841705, 'conceptrecid': '10841704', '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.10841705', 'recid': 10841705}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841705', 'html': 'https://zenodo.org/deposit/10841705', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841705/files', 'bucket': 'https://zenodo.org/api/files/2b98d5de-e845-4941-a5bf-2301f374feb9', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841705', 'latest_draft_html': 'https://zenodo.org/deposit/10841705', 'publish': 'https://zenodo.org/api/deposit/depositions/10841705/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841705/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841705/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841705/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841705/actions/registerconceptdoi'}, 'record_id': 10841705, '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 cc796bc4 Last updated: 2024-03-19 19:54:35 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 377b9e46 Last updated: 2024-03-19 20:02:52 PDT

:information_source: See details

Zenodo records have been created successfully: 
 {'book': {'created': '2024-03-20T03:02:32.549887+00:00', 'modified': '2024-03-20T03:02:32.634278+00:00', 'id': 10841720, 'conceptrecid': '10841719', 'metadata': {'title': '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.10841720', 'recid': 10841720}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841720', 'html': 'https://zenodo.org/deposit/10841720', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841720/files', 'bucket': 'https://zenodo.org/api/files/7b572eed-7a1a-4297-aa69-7edc5fe1c74f', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841720', 'latest_draft_html': 'https://zenodo.org/deposit/10841720', 'publish': 'https://zenodo.org/api/deposit/depositions/10841720/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841720/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841720/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841720/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841720/actions/registerconceptdoi'}, 'record_id': 10841720, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'repository': {'created': '2024-03-20T03:02:38.469807+00:00', 'modified': '2024-03-20T03:02:38.633281+00:00', 'id': 10841722, 'conceptrecid': '10841721', '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.10841722', 'recid': 10841722}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841722', 'html': 'https://zenodo.org/deposit/10841722', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841722/files', 'bucket': 'https://zenodo.org/api/files/fb498229-af54-41cf-bac9-976343446e30', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841722', 'latest_draft_html': 'https://zenodo.org/deposit/10841722', 'publish': 'https://zenodo.org/api/deposit/depositions/10841722/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841722/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841722/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841722/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841722/actions/registerconceptdoi'}, 'record_id': 10841722, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'data': {'created': '2024-03-20T03:02:44.298540+00:00', 'modified': '2024-03-20T03:02:44.420422+00:00', 'id': 10841726, 'conceptrecid': '10841725', '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.10841726', 'recid': 10841726}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841726', 'html': 'https://zenodo.org/deposit/10841726', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841726/files', 'bucket': 'https://zenodo.org/api/files/52d582ce-3fd5-4346-84fb-b13eca19fd9b', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841726', 'latest_draft_html': 'https://zenodo.org/deposit/10841726', 'publish': 'https://zenodo.org/api/deposit/depositions/10841726/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841726/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841726/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841726/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841726/actions/registerconceptdoi'}, 'record_id': 10841726, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}, 'docker': {'created': '2024-03-20T03:02:49.972669+00:00', 'modified': '2024-03-20T03:02:50.064842+00:00', 'id': 10841728, 'conceptrecid': '10841727', '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.10841728', 'recid': 10841728}}, 'title': 'Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"', 'links': {'self': 'https://zenodo.org/api/deposit/depositions/10841728', 'html': 'https://zenodo.org/deposit/10841728', 'badge': 'https://zenodo.org/badge/doi/.svg', 'files': 'https://zenodo.org/api/deposit/depositions/10841728/files', 'bucket': 'https://zenodo.org/api/files/a0e4cc77-e31b-443f-82ce-ce5e5c575144', 'latest_draft': 'https://zenodo.org/api/deposit/depositions/10841728', 'latest_draft_html': 'https://zenodo.org/deposit/10841728', 'publish': 'https://zenodo.org/api/deposit/depositions/10841728/actions/publish', 'edit': 'https://zenodo.org/api/deposit/depositions/10841728/actions/edit', 'discard': 'https://zenodo.org/api/deposit/depositions/10841728/actions/discard', 'newversion': 'https://zenodo.org/api/deposit/depositions/10841728/actions/newversion', 'registerconceptdoi': 'https://zenodo.org/api/deposit/depositions/10841728/actions/registerconceptdoi'}, 'record_id': 10841728, 'owner': 262806, 'files': [], 'state': 'unsubmitted', 'submitted': False}}

neurolibre / neurolibre-reviews