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[REVIEW]: A scoping review of reproducible research practices in MRI #21

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roboneuro opened this issue Dec 23, 2023 · 157 comments
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@roboneuro
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Submitting author: @agahkarakuzu (Agah Karakuzu)
Repository: https://github.com/agahkarakuzu/mriscope
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @pbellec
Reviewers: @agahkarakuzu
Reproducible preprint: Pending
Repository archive: Pending
Data archive: Pending
Book archive: Pending
Docker archive: Pending

Status

status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/a54aeb597088ea358eeedce57e7f3285"><img src="https://neurolibre.org/papers/a54aeb597088ea358eeedce57e7f3285/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/a54aeb597088ea358eeedce57e7f3285/status.svg)](https://neurolibre.org/papers/a54aeb597088ea358eeedce57e7f3285)

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

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

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

@roboneuro commands

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

@roboneuro generate pdf

@roboneuro
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Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (367.1 files/s, 105253.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             53              8           1989
Jupyter Notebook                 3              0           2090            499
Python                           7             72            141            176
YAML                             2             10              1             58
Markdown                         3              6              0             36
CSS                              1              1              0             17
JSON                             1              0              0              4
-------------------------------------------------------------------------------
SUM:                            18            142           2240           2779
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@roboneuro
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Wordcount for paper.md is 146

@roboneuro
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Failed to discover a Statement of need section in paper

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

OK DOIs

- None

MISSING DOIs

- 10.1101/2021.12.27.474259 may be a valid DOI for title: Vendor-neutral sequences and fully transparent workflows improve inter-vendor reproducibility of quantitative MRI
- 10.1002/mrm.28880 may be a valid DOI for title: Accelerated calibrationless parallel transmit mapping using joint transmit and receive low-rank tensor completion
- 10.3389/fphys.2023.1281147 may be a valid DOI for title: The relaxometry hype cycle
- 10.1002/jmri.26785 may be a valid DOI for title: Assessing effects of scanner upgrades for clinical studies
- 10.1002/mrm.28908 may be a valid DOI for title: Image- versus histogram-based considerations in semantic segmentation of pulmonary hyperpolarized gas images
- 10.18653/v1/2020.acl-main.207 may be a valid DOI for title: SPECTER: Document-level Representation Learning using Citation-informed Transformers
- 10.1002/mrm.26089 may be a valid DOI for title: ISMRM Raw data format: A proposed standard for MRI raw datasets
- 10.21105/joss.02343 may be a valid DOI for title: qMRLab: Quantitative MRI analysis, under one umbrella
- 10.1002/mrm.27984 may be a valid DOI for title: Steady-state imaging with inhomogeneous magnetization transfer contrast using multiband radiofrequency pulses
- 10.1002/mrm.26235 may be a valid DOI for title: Pulseq: A rapid and hardware-independent pulse sequence prototyping framework
- 10.1097/xeb.0000000000000050 may be a valid DOI for title: Guidance for conducting systematic scoping reviews
- 10.1038/sdata.2016.44 may be a valid DOI for title: The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments
- 10.1002/mrm.28678 may be a valid DOI for title: PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images
- 10.1002/mrm.28192 may be a valid DOI for title: A novel gamma GLM approach to MRI relaxometry comparisons
- 10.1371/journal.pcbi.1008725 may be a valid DOI for title: On the open-source landscape of PLOS Computational Biology
- 10.1002/mrm.28235 may be a valid DOI for title: Extreme MRI: Large-scale volumetric dynamic imaging from continuous non-gated acquisitions
- 10.1002/mrm.28997 may be a valid DOI for title: Accurate free-water estimation in white matter from fast diffusion MRI acquisitions using the spherical means technique
- 10.1002/mrm.29159 may be a valid DOI for title: VESPA ASL: VElocity and SPAtially Selective Arterial Spin Labeling
- 10.31219/osf.io/pu5vb may be a valid DOI for title: Open and reproducible neuroimaging: From study inception to publication
- 10.1002/mrm.29044 may be a valid DOI for title: Deep neural network based CEST and AREX processing: Application in imaging a model of Alzheimer’s disease at 3 T
- 10.1186/1748-5908-5-69 may be a valid DOI for title: Scoping studies: advancing the methodology
- 10.1002/mrm.29130 may be a valid DOI for title: Integration of an RF coil and commercial field camera for ultrahigh-field MRI
- 10.1002/mrm.28465 may be a valid DOI for title: RARE two-point Dixon with dual bandwidths
- 10.1002/mrm.27939 may be a valid DOI for title: Reproducibility and the future of MRI research
- 10.1002/mrm.28163 may be a valid DOI for title: FatSegNet: A fully automated deep learning pipeline for adipose tissue segmentation on abdominal dixon MRI
- 10.1002/uog.6276 may be a valid DOI for title: Cerebral biometry in fetal magnetic resonance imaging: new reference data
- 10.1002/mrm.28733 may be a valid DOI for title: Analysis of deep complex-valued convolutional neural networks for MRI reconstruction and phase-focused applications
- 10.1002/mrm.27910 may be a valid DOI for title: Deep learning how to fit an intravoxel incoherent motion model to diffusion-weighted MRI
- 10.1002/mrm.28259 may be a valid DOI for title: Myelin water fraction estimation using small-tip fast recovery MRI
- 10.1101/2020.07.24.214551 may be a valid DOI for title: Phase unwrapping with a rapid opensource minimum spanning tree algorithm (ROMEO)
- 10.1101/2020.06.16.155291 may be a valid DOI for title: FSL-MRS: An end-to-end spectroscopy analysis package
- 10.1002/mrm.28020 may be a valid DOI for title: Portable and platform-independent MR pulse sequence programs
- 10.58530/2022/2707 may be a valid DOI for title: Generalized Bloch model: A theory for pulsed magnetization transfer
- 10.1080/1364557032000119616 may be a valid DOI for title: Scoping studies: towards a methodological framework

INVALID DOIs

- None

@agahkarakuzu
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@roboneuro build book

@agahkarakuzu
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@roboneuro commands

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


# List all available commands
@roboneuro commands

# Add to this issue's reviewers list
@roboneuro add @username as reviewer

# Remove from this issue's reviewers list
@roboneuro remove @username from reviewers

# Get a list of all editors's GitHub handles
@roboneuro list editors

# Assign a user as the editor of this submission
@roboneuro assign @username as editor

# Remove the editor assigned to this submission
@roboneuro remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@roboneuro remind @reviewer in 2 weeks

# Check the references of the PDF for missing DOIs
@roboneuro check references

# Perform checks on the repository
@roboneuro check repository

# Adds a checklist for the reviewer using this command
@roboneuro generate my checklist

# Set a value for version
@roboneuro set v1.0.0 as version

# Set a value for branch
@roboneuro set neurolibre-paper as branch

# Set a value for repository
@roboneuro set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@roboneuro set set 10.5281/zenodo.6861996 as archive

# Set a value for the (data/book/repository/docker) archive DOI.
@roboneuro set 10.5281/zenodo.6861996 as data archive

# Set executable book URI for the preprint.
@roboneuro set book uri

# Mention the EiCs for the correct track
@roboneuro ping track-eic

# Reject paper
@roboneuro reject

# Withdraw paper
@roboneuro withdraw

# Invite an editor to edit a submission (sending them an email)
@roboneuro invite @(.*) as editor

# Generates the pdf paper
@roboneuro generate pdf

# Recommends the submission for acceptance
@roboneuro recommend-accept

# Accept and publish the paper
@roboneuro accept

# Update data on an accepted/published paper
@roboneuro reaccept

# Generates a LaTeX preprint file
@roboneuro generate preprint

# Flag submission with questionable scope
@roboneuro query scope

# Get a link to the complete list of reviewers
@roboneuro list reviewers

# Creates a post-review checklist with editor and authors tasks
@roboneuro create post-review checklist

# Open the review issue
@roboneuro start review

# Check the status of the NeuroLibre preview server.
@roboneuro preview server status

# Check the status of the NeuroLibre preprint (production) server.
@roboneuro preprint server status

# Build a NeuroLibre reproducible preprint for technical screening.
@roboneuro build book

# After screening, build book from the forked reository.
@roboneuro production build book

# Transfer data from preview to the preprint (production) server.
@roboneuro production sync data

# Transfer the final preprint (forked repo) to the preprint (production) server (DOI URL).
@roboneuro production sync book

# Start the production process by forking repository and configuring it.
@roboneuro production start

# Creates Zenodo deposits (a.k.a buckets) for archiving reproducibility assets.
@roboneuro zenodo create buckets

# Status check for the archival of the reproducibility assets.
@roboneuro zenodo status

# Copy summary PDF from the preprints repository to the NeuroLibre production server.
@roboneuro production sync pdf

# Upload the latest Jupyter Book to Zenodo for archival.
@roboneuro zenodo upload book

# Upload the latest version of the book repository to Zenodo for archival.
@roboneuro zenodo upload repository

# Upload the latest version of the docker image to Zenodo for archival.
@roboneuro zenodo upload docker

# Upload the submission data to Zenodo for archival. Will not take effect if the data is already archived.
@roboneuro zenodo upload data

# DESTRUCTIVE ACTION: Deletes zenodo records and all the data that has been uploaded. Cannot perform after zenodo publish.
@roboneuro zenodo flush

# Publish reproducibility assets on Zenodo. Sets DOIs if successful.
@roboneuro zenodo publish

# Build an extended PDF for the target repository.
@roboneuro build extended pdf

@roboneuro
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@agahkarakuzu
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@roboneuro build book

@agahkarakuzu
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@roboneuro preview server status

@roboneuro
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🟢 NeuroLibre server is active (running).
🍀 Ready to accept requests from Issue #21
🔗 URL: https://preview.neurolibre.org

@agahkarakuzu
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@roboneuro build book

@roboneuro
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Book Build (Preview)

Status: Waiting for task assignment
Last updated: 2023-12-24 13:52:12 PST

♻️ Refresh

@agahkarakuzu
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@roboneuro build book

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roboneuro commented Dec 24, 2023

🟢 Successfully built

Status: Success a969eda5
Last updated: 2023-12-24 14:02:20 PST

ℹ️ See details
:confetti_ball: Roboneuro will send you the book URL.

@roboneuro
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🤖💬🎊🚀
Congratulations to the authors on their neurolibre reproducible preprint (NRP)! Their MRI-scoping review is sure to make a memorable 'brain-print' in the scientific community, emphasizing reproducibility as the key ingredient for mind-boggling research.

🌺 Take a loot at the latest version of your NRP! 🌺

Important

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

@agahkarakuzu
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@roboneuro build book

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roboneuro commented Dec 24, 2023

🟢 Successfully built

Status: Success 9df30343
Last updated: 2023-12-24 14:21:20 PST

ℹ️ See details
:confetti_ball: Roboneuro will send you the book URL.

@roboneuro
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🤖💬🎊🚀
Congratulations to the authors on successfully unlocking the mysteries of reproducibility in MRI with their neurolibre reproducible preprint (NRP)! They've captured the brain's essence, replicability, and made us all MRIreverent.

🌺 Take a loot at the latest version of your NRP! 🌺

Important

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

@agahkarakuzu
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Member

@roboneuro commands

@roboneuro
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Author

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


# List all available commands
@roboneuro commands

# Add to this issue's reviewers list
@roboneuro add @username as reviewer

# Remove from this issue's reviewers list
@roboneuro remove @username from reviewers

# Get a list of all editors's GitHub handles
@roboneuro list editors

# Assign a user as the editor of this submission
@roboneuro assign @username as editor

# Remove the editor assigned to this submission
@roboneuro remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@roboneuro remind @reviewer in 2 weeks

# Check the references of the PDF for missing DOIs
@roboneuro check references

# Perform checks on the repository
@roboneuro check repository

# Adds a checklist for the reviewer using this command
@roboneuro generate my checklist

# Set a value for version
@roboneuro set v1.0.0 as version

# Set a value for branch
@roboneuro set neurolibre-paper as branch

# Set a value for repository
@roboneuro set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@roboneuro set set 10.5281/zenodo.6861996 as archive

# Set a value for the (data/book/repository/docker) archive DOI.
@roboneuro set 10.5281/zenodo.6861996 as data archive

# Set executable book URI for the preprint.
@roboneuro set book uri

# Mention the EiCs for the correct track
@roboneuro ping track-eic

# Reject paper
@roboneuro reject

# Withdraw paper
@roboneuro withdraw

# Invite an editor to edit a submission (sending them an email)
@roboneuro invite @(.*) as editor

# Generates the pdf paper
@roboneuro generate pdf

# Recommends the submission for acceptance
@roboneuro recommend-accept

# Accept and publish the paper
@roboneuro accept

# Update data on an accepted/published paper
@roboneuro reaccept

# Generates a LaTeX preprint file
@roboneuro generate preprint

# Flag submission with questionable scope
@roboneuro query scope

# Get a link to the complete list of reviewers
@roboneuro list reviewers

# Creates a post-review checklist with editor and authors tasks
@roboneuro create post-review checklist

# Open the review issue
@roboneuro start review

# Check the status of the NeuroLibre preview server.
@roboneuro preview server status

# Check the status of the NeuroLibre preprint (production) server.
@roboneuro preprint server status

# Build a NeuroLibre reproducible preprint for technical screening.
@roboneuro build book

# After screening, build book from the forked reository.
@roboneuro production build book

# Transfer data from preview to the preprint (production) server.
@roboneuro production sync data

# Transfer the final preprint (forked repo) to the preprint (production) server (DOI URL).
@roboneuro production sync book

# Start the production process by forking repository and configuring it.
@roboneuro production start

# Creates Zenodo deposits (a.k.a buckets) for archiving reproducibility assets.
@roboneuro zenodo create buckets

# Status check for the archival of the reproducibility assets.
@roboneuro zenodo status

# Copy summary PDF from the preprints repository to the NeuroLibre production server.
@roboneuro production sync pdf

# Upload the latest Jupyter Book to Zenodo for archival.
@roboneuro zenodo upload book

# Upload the latest version of the book repository to Zenodo for archival.
@roboneuro zenodo upload repository

# Upload the latest version of the docker image to Zenodo for archival.
@roboneuro zenodo upload docker

# Upload the submission data to Zenodo for archival. Will not take effect if the data is already archived.
@roboneuro zenodo upload data

# DESTRUCTIVE ACTION: Deletes zenodo records and all the data that has been uploaded. Cannot perform after zenodo publish.
@roboneuro zenodo flush

# Publish reproducibility assets on Zenodo. Sets DOIs if successful.
@roboneuro zenodo publish

# Build an extended PDF for the target repository.
@roboneuro build extended pdf

# Download the submission data.
@roboneuro cache data

@agahkarakuzu
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@roboneuro cache data

@agahkarakuzu
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@roboneuro build latest myst at runtime 4ca41ea355ee634d06f3274e81e2e994e16cef6f

@roboneuro
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roboneuro commented Nov 20, 2024

🟢 Build MyST article

Status: Success 2e4d817d
Last updated: 2024-11-20 10:22:31 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/mriscope/4ca41ea355ee634d06f3274e81e2e994e16cef6f/_build/html/index.html

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roboneuro commented Nov 20, 2024

🔴 Build MyST article

Status: Failed 38731a39
Last updated: 2024-11-20 11:35:23 PST

Problem reading myst.yml

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roboneuro commented Nov 20, 2024

🔴 Build MyST article

Status: Failed 25b1ef13
Last updated: 2024-11-20 11:39:50 PST

Problem reading myst.yml

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roboneuro commented Nov 20, 2024

🟠 Build MyST article

Status: In progress afd49cf9
Last updated: 2024-11-20 11:47:25 PST

ℹ️ See details
Cloning repository, pulling binder image, spawning JupyterHub...
♻️ Refresh

@roboneuro
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roboneuro commented Nov 20, 2024

🔴 Build MyST article

Status: Failed 9dd12403
Last updated: 2024-11-20 12:09:55 PST

MyST build failed did not produce the expected webpage.

@roboneuro
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roboneuro commented Nov 20, 2024

🔴 Build MyST article

Status: Failed f0cf1a54
Last updated: 2024-11-20 12:38:33 PST

MyST build failed did not produce the expected webpage.

@roboneuro
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roboneuro commented Nov 20, 2024

🔴 Build MyST article

Status: Failed 29672c9a
Last updated: 2024-11-20 12:49:47 PST

MyST build failed did not produce the expected webpage.

@roboneuro
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roboneuro commented Nov 21, 2024

🟠 Build MyST article

Status: In progress 40f72e67
Last updated: 2024-11-21 09:38:31 PST

ℹ️ See details
Issuing MyST build command, execution environment: binder-registry.conp.cloud/binder-neurolibre-2dmystical-2darticle-72300d
♻️ Refresh

@roboneuro
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roboneuro commented Nov 21, 2024

🔴 Build MyST article

Status: Failed db0ed748
Last updated: 2024-11-21 09:53:33 PST

MyST build failed did not produce the expected webpage.

@roboneuro
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roboneuro commented Nov 23, 2024

🔴 Build MyST article

Status: Failed 29fecc85
Last updated: 2024-11-23 03:55:00 PST

MyST build failed did not produce the expected webpage.

@roboneuro
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roboneuro commented Nov 23, 2024

🔴 Build MyST article

Status: Failed bc845978
Last updated: 2024-11-23 04:00:38 PST

MyST build failed did not produce the expected webpage.

@roboneuro
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roboneuro commented Nov 25, 2024

🔴 Build MyST article

Status: Failed a013f41c
Last updated: 2024-11-25 07:31:14 PST

MyST build failed did not produce the expected webpage.

@agahkarakuzu
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@roboneuro build latest myst at runtime 4ca41ea355ee634d06f3274e81e2e994e16cef6f

@roboneuro
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roboneuro commented Nov 25, 2024

🟠 Build MyST article

Status: In progress b302affb
Last updated: 2024-11-25 07:58:45 PST

ℹ️ See details
Issuing MyST build command, execution environment: binder-registry.conp.cloud/binder-agahkarakuzu-2dmriscope-7a73fb
♻️ Refresh

@roboneuro
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roboneuro commented Nov 25, 2024

🟢 Build MyST article

Status: Success 64d219ca
Last updated: 2024-11-25 08:11:46 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/neurolibre/mystical-article/66bba73ee1b8093e2eac2818ecd69f695ff085d6/_build/html/index.html

@agahkarakuzu
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@roboneuro build latest myst at runtime latest

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roboneuro commented Nov 25, 2024

🟠 Build MyST article

Status: In progress fd80c877
Last updated: 2024-11-25 08:16:21 PST

ℹ️ See details
Initiating ✨MyST✨ build...
♻️ Refresh

@agahkarakuzu
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@roboneuro generate pdf

@agahkarakuzu
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@roboneuro build latest myst at runtime latest

@roboneuro
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roboneuro commented Nov 26, 2024

🟠 Build MyST article

Status: In progress c45c013a
Last updated: 2024-11-25 17:27:44 PST

ℹ️ See details
Initiating ✨MyST✨ build...
♻️ Refresh

@roboneuro
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@agahkarakuzu
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@roboneuro build latest myst at runtime latest

@roboneuro
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roboneuro commented Nov 26, 2024

🟢 Build MyST article

Status: Success 1bf0e4aa
Last updated: 2024-11-25 17:41:45 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/mriscope/6e6330efbd6e6011f1c068822fc8cda482f28ef8/_build/html/index.html

@agahkarakuzu
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@roboneuro build latest myst at runtime latest

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roboneuro commented Nov 26, 2024

🟢 Build MyST article

Status: Success cd4a7217
Last updated: 2024-11-25 18:46:59 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/mriscope/24a80e4c95ececbd3b4ee08892e0905ee73d35a8/_build/html/index.html

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@roboneuro production start

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roboneuro commented Dec 15, 2024

🔴 INITIATE PRODUCTION (Fork and Configure)

Status: Failed 776046fe
Last updated: 2024-12-15 17:37:30 EST

Warning

A living preprint build could not be found at commit 24a80e4c95ececbd3b4ee08892e0905ee73d35a8 at https://github.com/agahkarakuzu/mriscope. Production process cannot be started.

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@roboneuro production start

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roboneuro commented Dec 15, 2024

🟢 INITIATE PRODUCTION (Fork and Configure)

Status: Success 30ccb0f6
Last updated: 2024-12-15 17:40:14 EST

ℹ️ See details
Please confirm that the forked repository is available and (myst.yml) properly configured.

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