Beyond advertising: New infrastructures for publishing integrated research objects

DuPré, Elizabeth; Holdgraf, Chris; Karakuzu, Agâh; Tetrel, Loïc; Bellec, Pierre; Stikov, Nikola; Poline, Jean‐Baptiste

doi:10.1371/journal.pcbi.1009651

Cited by 15 publications

(10 citation statements)

References 19 publications

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“…We argue that this is a reasonable trade‐off as it peels another layer from a vendor‐specific ecosystem, and it does not sacrifice the transparency of sources relevant to a pulse sequence description. The accuracy and reliability of the parameter estimation depend on these descriptions; therefore, for qMRI to work we need to be able to access, modify, and share the methods 68 . Fortunately, the VENUS approach to qMRI is not framework‐exclusive and satisfies this key requirement.…”

Section: Discussionmentioning

confidence: 99%

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Vendor‐neutral sequences and fully transparent workflows improve inter‐vendor reproducibility of quantitative MRI

Karakuzu

Biswas

Cohen‐Adad

et al. 2022

Magnetic Resonance in Med

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Purpose We developed an end‐to‐end workflow that starts with a vendor‐neutral acquisition and tested the hypothesis that vendor‐neutral sequences decrease inter‐vendor variability of T1, magnetization transfer ratio (MTR), and magnetization transfer saturation‐index (MTsat) measurements. Methods We developed and deployed a vendor‐neutral 3D spoiled gradient‐echo (SPGR) sequence on three clinical scanners by two MRI vendors. We then acquired T1 maps on the ISMRM‐NIST system phantom, as well as T1, MTR, and MTsat maps in three healthy participants. We performed hierarchical shift function analysis in vivo to characterize the differences between scanners when the vendor‐neutral sequence is used instead of commercial vendor implementations. Inter‐vendor deviations were compared for statistical significance to test the hypothesis. Results In the phantom, the vendor‐neutral sequence reduced inter‐vendor differences from 8% to 19.4% to 0.2% to 5% with an overall accuracy improvement, reducing ground truth T1 deviations from 7% to 11% to 0.2% to 4%. In vivo, we found that the variability between vendors is significantly reduced (p = 0.015) for all maps (T1, MTR, and MTsat) using the vendor‐neutral sequence. Conclusion We conclude that vendor‐neutral workflows are feasible and compatible with clinical MRI scanners. The significant reduction of inter‐vendor variability using vendor‐neutral sequences has important implications for qMRI research and for the reliability of multicenter clinical trials.

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Section: Discussionmentioning

confidence: 99%

“…The accuracy and reliability of the parameter estimation depend on these descriptions; therefore, for qMRI to work we need to be able to access, modify, and share the methods. 68 Fortunately, the VENUS approach to qMRI is not framework-exclusive and satisfies this key requirement.…”

Section: Implications Of Vendor Neutrality and The Importance Of Tran...mentioning

confidence: 99%

Vendor‐neutral sequences and fully transparent workflows improve inter‐vendor reproducibility of quantitative MRI

Karakuzu

Biswas

Cohen‐Adad

et al. 2022

Magnetic Resonance in Med

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“…Quantitative MRI is in a dire need of standardization from scanner to the publication 56 of integrated research objects 57 to reach its full potential. The data standard developed by the present work provides an important stepping stone towards achieving this wider objective.…”

Section: Discussionmentioning

confidence: 99%

qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data

et al. 2022

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The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store multimodal structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI through multicenter dissemination of interoperable datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. In conclusion, this BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the entrance barrier for qMRI in the field of neuroimaging.

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“…In this work, authors provided alongside the traditional research paper a Jupyter notebook that performed and documented the entire analysis procedure. The MyST (short for Markedly Structured Text notebook) is built on top of Jupyter notebooks or Markdown documents and has some notable advantages around flexibility of content that make it an attractive choice for executable article authoring [ 27 ].…”

Section: Recommendationsmentioning

confidence: 99%

The five pillars of computational reproducibility: bioinformatics and beyond

Ziemann,

Poulain,

Bora

2023

Briefings in Bioinformatics

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Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) literate programming, (2) code version control and sharing, (3) compute environment control, (4) persistent data sharing and (5) documentation. These practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatics data analysts and bioinformaticians in training, but should be relevant to other domains of study.

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Beyond advertising: New infrastructures for publishing integrated research objects

Cited by 15 publications

References 19 publications

Vendor‐neutral sequences and fully transparent workflows improve inter‐vendor reproducibility of quantitative MRI

Vendor‐neutral sequences and fully transparent workflows improve inter‐vendor reproducibility of quantitative MRI

qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data

The five pillars of computational reproducibility: bioinformatics and beyond

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