[REVIEW]: Paper is not enough: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge

[roboneuro]

Submitting author: @mathieuboudreau (Mathieu Boudreau)
Repository: https://www.github.com/rrsg2020/note
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @pbellec
Reviewers: @pbellec
Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00023
Repository archive: 10.5281/zenodo.10589600
Data archive: 10.5281/zenodo.10589602
Book archive: 10.5281/zenodo.10589598
Docker archive: 10.5281/zenodo.10589605

Status

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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

@pbellec, 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

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

[roboneuro]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (233.9 files/s, 98796.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
TeX                               1             54             12           1599
Jupyter Notebook                  1              0            878           1532
Markdown                          2             80              0            341
YAML                              4             13             17             62
CSS                               1              6              0             46
JSON                              1              0              0              5
Bourne Again Shell                1              0              0              2
--------------------------------------------------------------------------------
SUM:                             11            153            907           3587
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gitinspector failed to run statistical information for the repository

[roboneuro]

Wordcount for paper.md is 5322

[roboneuro]

Failed to discover a valid open source license

[roboneuro]

Failed to discover a Statement of need section in paper

[roboneuro]

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

[roboneuro]

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

OK DOIs

- None

MISSING DOIs

- 10.1371/journal.pone.0091318 may be a valid DOI for title: Rapid parametric mapping of the longitudinal relaxation time T1 using two-dimensional variable flip angle magnetic resonance imaging at 1.5 Tesla, 3 Tesla, and 7 Tesla
- 10.1118/1.595535 may be a valid DOI for title: A review of normal tissue hydrogen NMR relaxation times and relaxation mechanisms from 1-100 MHz: dependence on tissue type, NMR frequency, temperature, species, excision, and age
- 10.1186/1532-429x-12-69 may be a valid DOI for title: Shortened Modified Look-Locker Inversion recovery (ShMOLLI) for clinical myocardial T1-mapping at 1.5 and 3 T within a 9 heartbeat breathhold
- 10.1016/j.neuroimage.2021.117744 may be a valid DOI for title: Can MRI measure myelin? Systematic review, qualitative assessment, and meta-analysis of studies validating microstructural imaging with myelin histology
- 10.1088/0031-9155/23/5/012 may be a valid DOI for title: A line scan image study of a tumorous rat leg by NMR
- 10.1016/j.mri.2016.08.021 may be a valid DOI for title: What are normal relaxation times of tissues at 3 T?
- 10.1103/physrev.76.145 may be a valid DOI for title: An Accurate Nuclear Magnetic Resonance Method for Measuring Spin-Lattice Relaxation Times
- 10.1145/2723872.2723882 may be a valid DOI for title: An introduction to Docker for reproducible research
- 10.1002/mrm.1278.abs may be a valid DOI for title: Quantitative imaging of magnetization transfer exchange and relaxation properties in vivo using MRI
- 10.21105/joss.02343 may be a valid DOI for title: qMRLab: Quantitative MRI analysis, under one umbrella
- 10.1109/mcse.2021.3052101 may be a valid DOI for title: Using Jupyter for Reproducible Scientific Workflows
- 10.25080/majora-4af1f417-011 may be a valid DOI for title: Binder 2.0 - Reproducible, interactive, sharable environments for science at scale
- 10.1002/jmri.26598 may be a valid DOI for title: Recommendations towards standards for quantitative MRI (qMRI) and outstanding needs
- 10.1063/1.1684482 may be a valid DOI for title: Time saving in measurement of NMR and EPR relaxation times
- 10.1126/science.171.3976.1151 may be a valid DOI for title: Tumor detection by nuclear magnetic resonance
- 10.1002/mrm.28020 may be a valid DOI for title: Portable and platform-independent MR pulse sequence programs
- 10.1088/0370-1298/62/5/306 may be a valid DOI for title: A Direct Method of Measuring Nuclear Spin-Lattice Relaxation Times
- 10.1186/1532-429x-15-13 may be a valid DOI for title: Normal variation of magnetic resonance T1 relaxation times in the human population at 1.5 T using ShMOLLI
- 10.1016/b978-0-12-817057-1.00004-4 may be a valid DOI for title: Quantitative T1 and T1r Mapping
- 10.1002/jmri.1880070113 may be a valid DOI for title: Modeling tracer kinetics in dynamic Gd-DTPA MR imaging
- 10.1371/journal.pone.0252966 may be a valid DOI for title: Multi-site, multi-platform comparison of MRI T1 measurement using the system phantom
- 10.1002/(sici)1522-2586(199904)9:4<531::aid-jmri4>3.0.co;2-l may be a valid DOI for title: NMR relaxation times in the human brain at 3.0 tesla
- 10.1002/mrm.26235 may be a valid DOI for title: Pulseq: A rapid and hardware-independent pulse sequence prototyping framework
- 10.1016/j.neuroimage.2009.10.002 may be a valid DOI for title: MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field
- 10.1016/0730-725x(87)90021-x may be a valid DOI for title: Rapid calculation of T1 using variable flip angle gradient refocused imaging

INVALID DOIs

- None

[agahkarakuzu]

@roboneuro set 10.5281/zenodo.841980 as data archive