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arxiv: 1906.09996 · v1 · pith:CBXHTMIQnew · submitted 2019-06-24 · 💻 cs.DL · q-bio.NC

The BIDS Toolbox: A web service to manage brain imaging datasets

Unai Lopez-Novoa , Cyril Charron , John Evans , Leandro Beltrachini This is my paper

Pith reviewed 2026-05-25 16:46 UTC · model grok-4.3

classification 💻 cs.DL q-bio.NC
keywords BIDSneuroimagingMRIdata managementweb servicedata sharingbrain imaging
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The pith

The BIDS Toolbox is a web service for creating and modifying BIDS-compliant MRI datasets via web interface and REST endpoints.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper presents the BIDS Toolbox as a solution to increase adoption of the BIDS standard in neuroimaging. It claims that the lack of an easy-to-use tool has prevented wider use of BIDS for organizing MRI data. The toolbox supports dataset creation and changes through both a graphical web page and API endpoints. Readers might care because standardized data formats can make it easier to share and reproduce brain imaging experiments.

Core claim

The BIDS Toolbox allows the creation and modification of BIDS-compliant datasets based on MRI data. It provides both a web interface and REST endpoints for its use, unlike other tools.

What carries the argument

The BIDS Toolbox web service, which manages brain imaging datasets in BIDS format through creation and modification features.

If this is right

  • Users can create BIDS-compliant datasets from MRI data more straightforwardly.
  • The service supports both interactive web use and programmatic access via REST.
  • Early prototype is available with public source code.
  • BIDS datasets can be managed in a way that promotes data sharing.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Integration with existing MRI analysis pipelines could further boost usability.
  • Wider adoption might improve reproducibility across studies if the tool proves effective.
  • Future versions could extend support to other imaging modalities beyond MRI.

Load-bearing premise

Low adoption of BIDS stems mainly from the absence of a primary tool for creating and managing such datasets.

What would settle it

A survey or usage analysis showing that BIDS adoption remains low even after the release and promotion of the BIDS Toolbox would challenge the premise.

Figures

Figures reproduced from arXiv: 1906.09996 by Cyril Charron, John Evans, Leandro Beltrachini, Unai Lopez-Novoa.

Figure 1
Figure 1. Figure 1: Algorithm to detect scan type of a series of images. FA stands for Flip Angle, IR for Inversion Recovery, SS for Scanning Sequence, TE for Echo [PITH_FULL_IMAGE:figures/full_fig_p003_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Screenshot of the web front-end for the BIDS Toolbox. [PITH_FULL_IMAGE:figures/full_fig_p004_2.png] view at source ↗
read the original abstract

Data sharing is a key factor for ensuring reproducibility and transparency of scientific experiments, and neuroimaging is no exception. The vast heterogeneity of data formats and imaging modalities utilised in the field makes it a very challenging problem. In this context, the Brain Imaging Data Structure (BIDS) appears as a solution for organising and describing neuroimaging datasets. Since its publication in 2015, BIDS has gained widespread attention in the field, as it provides a common way to arrange and share multimodal brain images. Although the evident benefits it presents, BIDS has not been widely adopted in the field of MRI yet and we believe that this is due to the lack of a go-to tool to create and managed BIDS datasets. Motivated by this, we present the BIDS Toolbox, a web service to manage brain imaging datasets in BIDS format. Different from other tools, the BIDS Toolbox allows the creation and modification of BIDS-compliant datasets based on MRI data. It provides both a web interface and REST endpoints for its use. In this paper we describe its design and early prototype, and provide a link to the public source code repository.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 1 minor

Summary. The manuscript describes the BIDS Toolbox, a web service for creating and modifying BIDS-compliant MRI datasets. It provides both a web interface and REST endpoints, positions itself as addressing a gap in BIDS adoption tools, and reports the design of an early prototype along with a link to the public source code repository.

Significance. If the described functionality is accurate, the tool could lower barriers to BIDS dataset management in neuroimaging. The public availability of the source code is a clear strength for a software-description paper, as it permits direct inspection, reuse, and community validation of the implementation.

major comments (2)
  1. [Abstract] Abstract: the claim that the BIDS Toolbox 'differs from other tools' by enabling creation and modification of BIDS datasets is stated without any reference to or comparison against existing BIDS-related software, leaving the distinctiveness of the contribution unsupported.
  2. [Abstract] Abstract and manuscript body: no evaluation, usage examples, error-handling details, or BIDS-compliance verification steps are described for the early prototype, which weakens assessment of the central claim that the service is usable for dataset management.
minor comments (1)
  1. [Abstract] Abstract: grammatical issues include 'Although the evident benefits it presents' (should read 'Despite the evident benefits' or similar) and 'create and managed' (should be 'create and manage').

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for the positive summary and recommendation for minor revision. We address each major comment below and indicate where revisions will be made to the manuscript.

read point-by-point responses

  1. Referee: [Abstract] Abstract: the claim that the BIDS Toolbox 'differs from other tools' by enabling creation and modification of BIDS datasets is stated without any reference to or comparison against existing BIDS-related software, leaving the distinctiveness of the contribution unsupported.

    Authors: We agree that the distinctiveness claim in the abstract would be strengthened by explicit references to existing BIDS tools. In the revised manuscript we will add a short comparison (with citations) to tools such as dcm2bids, BIDScoin, and the official BIDS validator, clarifying that the BIDS Toolbox is distinguished by its focus on web-based creation and in-place modification via both a GUI and REST API. This addition will be limited to the abstract and a brief paragraph in the introduction. revision: yes

  2. Referee: [Abstract] Abstract and manuscript body: no evaluation, usage examples, error-handling details, or BIDS-compliance verification steps are described for the early prototype, which weakens assessment of the central claim that the service is usable for dataset management.

    Authors: The manuscript is explicitly framed as describing the design and an early prototype; therefore a full user evaluation was not performed. We will nevertheless add a new subsection with concrete usage examples (including sample API calls and web-interface workflows) and a description of the current error-handling approach and BIDS-compliance checks implemented in the prototype. Because the source code is already public, readers can inspect and test these aspects directly. A comprehensive usability study remains outside the scope of this software-description paper. revision: partial

Circularity Check

0 steps flagged

No significant circularity

full rationale

This manuscript is a software description paper presenting the design of the BIDS Toolbox prototype and a link to its public source code. It contains no derivations, equations, fitted parameters, predictions, or first-principles results of any kind. The central claim (that the tool enables creation and modification of BIDS-compliant MRI datasets via web and REST interfaces) is supported directly by the prototype implementation itself, with no load-bearing steps that reduce to self-citation chains, ansatzes, or renamings. The motivational premise about BIDS adoption is not required for the functionality claim and does not participate in any derivation. The work is therefore self-contained against external benchmarks such as shipped code.

Axiom & Free-Parameter Ledger

0 free parameters · 0 axioms · 0 invented entities

The paper is a software-tool description with no mathematical model, no fitted parameters, and no new physical or theoretical entities. The only background assumptions are standard software-engineering practices and the existence of the BIDS specification itself.

pith-pipeline@v0.9.0 · 5739 in / 1120 out tokens · 21404 ms · 2026-05-25T16:46:39.623900+00:00 · methodology

discussion (0)

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