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

Open roboneuro opened 6 months ago

roboneuro commented 6 months ago

Submitting author: !--author-handle-->@agahkarakuzu<!--end-author-handle-- (Agah Karakuzu) Repository: https://github.com/agahkarakuzu/mriscope Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@pbellec<!--end-editor-- Reviewers: !--reviewers-list-->@agahkarakuzu<!--end-reviewers-list-- 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 commented 6 months ago

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 commented 6 months ago 
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 commented 6 months ago

Wordcount for paper.md is 146

roboneuro commented 6 months ago

Failed to discover a Statement of need section in paper

roboneuro commented 6 months ago 
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 commented 6 months ago

@roboneuro build book

agahkarakuzu commented 6 months ago

@roboneuro commands

roboneuro commented 6 months ago

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 commented 6 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 6 months ago

@roboneuro build book

agahkarakuzu commented 6 months ago

@roboneuro preview server status

roboneuro commented 6 months ago

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

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

⚫ Book Build (Preview)

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

:recycle: Refresh

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

🟢 Successfully built

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

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 6 months ago

:robot::speech_balloon::confetti_ball::rocket: 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.

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

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

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

🟢 Successfully built

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

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 6 months ago

:robot::speech_balloon::confetti_ball::rocket: 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.

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

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

agahkarakuzu commented 6 months ago

@roboneuro commands

roboneuro commented 6 months ago

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 commented 6 months ago

@roboneuro cache data

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

🟢 Successfully built

Status: Success 4d38f4ca Last updated: 2023-12-27 10:18:45 PST

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 6 months ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on successfully building the neurolibre reproducible preprint (NRP)! With the MRI-focused scoping review, their research has clearly crossed the "brain" barrier and laid the foundation for more reproducible studies in the field.

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

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

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

🟢 Successfully built

Status: Success 252c2b92 Last updated: 2023-12-27 10:31:21 PST

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 6 months ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for crafting the neurolibre reproducible preprint (NRP)! With their MRI, they have skillfully imaged the realm of reproducibility, producing a comprehensive scoping review that will undoubtedly leave an indelible Mark on the scientific community. 🧠🔬

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

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

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

🟢 Successfully built

Status: Success 56bb01cd Last updated: 2023-12-27 10:56:37 PST

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 6 months ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on their remarkable neurolibre reproducible preprint (NRP)! With the power of MRI, they've not only captured brain images but also managed to scan the realm of reproducibility, paving the way for more transparent and reliable research practices.

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

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

agahkarakuzu commented 6 months ago

@roboneuro build book

roboneuro commented 6 months ago

🟢 Successfully built

Status: Success fb831bdf Last updated: 2023-12-27 11:13:10 PST

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 6 months ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on constructing the Neurolibre Reproducible Preprint (NRP)! With the power to unveil MRI research practices and ensure their reproducibility, it seems like they've cracked the code to make minds resonate with every scan. Well done!

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

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