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Estrella-231
Estrella-231COMMUNITY
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bids

Organize neuroscience and biomedical data into BIDS-compliant directory structures.

Updated May 24, 2026
Search Tags:#data validation#neuroimaging#bids#metadata sidecars#dicom to bids#dataset organization
One-click install
npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill bids-estrella-231
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bids
Source: https://github.com/Estrella-231/Mathematical_modeling_tongmeng/tree/main/.agents/skills/bids
Command: npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill bids-estrella-231

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

BIDS reduces friction in sharing, searching, and processing neuroscience/biomedical datasets by enforcing a consistent directory structure and metadata conventions; this skill helps you validate compliance, query layouts, convert DICOM to BIDS, and manage derivatives.

Core Features & Use Cases

  • BIDS-compliant dataset structuring: Create or reorganize data using the required sub-*/datatype directory hierarchy and standardized filenames.
  • Query and metadata access: Use PyBIDS layout indexing to retrieve files by subject/session/task/run and read JSON sidecar metadata (with inheritance).
  • Validation and conversion: Run BIDS validation and convert DICOM to BIDS using common toolchains (HeuDiConv, dcm2bids, BIDScoin), including sidecar handling and derivatives setup.
  • Derivatives management: Produce and describe processed outputs under derivatives/ with correct dataset_description.json.

Quick Start

Use the bids skill to validate that your dataset at /path/to/bids_dataset follows the BIDS specification and report any compliance issues.

Frequently Asked Questions about bids

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert DICOM files to BIDS format for neuroimaging datasets?▼

To convert DICOM to BIDS, you can use common toolchains like HeuDiConv, dcm2bids, or BIDScoin to organize data into the required sub-* directory hierarchy while handling JSON metadata sidecars.

What is BIDS validation and how does it check dataset compliance?▼

BIDS validation checks your dataset's compliance with the BIDS specification by enforcing the correct directory hierarchy, standardized filenames, and required root-level dataset_description.json metadata.

How do I query and access BIDS metadata using PyBIDS?▼

PyBIDS layout indexing allows you to retrieve files by subject, session, task, or run parameters and read JSON sidecar metadata while respecting the inheritance principle across the dataset.

How do I organize processed neuroimaging outputs as BIDS derivatives?▼

To manage BIDS derivatives, place processed outputs under the derivatives/ directory and describe them with a correct dataset_description.json file to ensure proper downstream sharing and analysis.

Can I use BIDS to organize multiple neuroimaging modalities like MRI, EEG, and PET?▼

Yes, BIDS supports organizing common modalities including MRI, EEG, MEG, PET, microscopy, and behavioral records by enforcing a consistent directory structure and metadata conventions across all data types.

Why does my BIDS dataset fail validation when checking metadata sidecars?▼

BIDS validation fails when the dataset lacks correct root-level dataset_description metadata, violates the sub-* directory hierarchy, or contains JSON sidecar inheritance errors that do not match the specification.

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