skills.rest
tassiovale
tassiovaleCOMMUNITY
Explore all skills by this author →
WebsiteGitHub

bids

Organize, query, validate, and convert neuroscience data into BIDS-compliant datasets.

13|3|Updated Jun 10, 2026
Search Tags:#data processing#neuroscience#data organization#biomedicine#dataset conversion#bids
One-click install
npx skills add https://github.com/tassiovale/claude-code-kit --skill bids-tassiovale
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bids
Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/bids
Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill bids-tassiovale

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pybids, bids-validator, heudiconv, dcm2bids, nibabel, pydicom, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill simplifies the organization, querying, and processing of BIDS datasets, making neuroscience and biomedical data more accessible and manageable.

Core Features & Use Cases

  • BIDS Organization: Structure raw neuroscience data into BIDS-compliant directory structures.
  • Data Querying: Efficiently query BIDS datasets for specific files based on subject, session, task, run, or modality.
  • Data Validation: Validate BIDS datasets against the BIDS specification to ensure compliance.
  • DICOM Conversion: Convert DICOM data to BIDS format for consistent data representation.
  • Metadata Management: Write and edit JSON sidecar metadata files for BIDS datasets.
  • Derivative Creation: Create BIDS-compliant derivatives (preprocessed data, analysis outputs).
  • Use Case: If you have raw EEG data and want to convert it into a BIDS-compliant format for analysis with existing BIDS tools, this Skill can guide you through the process.

Quick Start

Use the bids skill to convert a DICOM directory to BIDS format with the command: bids convert /path/to/dicom /path/to/bids_output

Frequently Asked Questions about bids

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

FAQPage Schema
How do I convert DICOM data to BIDS format for neuroscience research?▼

To convert DICOM data to BIDS format, you provide a DICOM directory and an output path to automate the transformation. This process uses tools like HeuDiConv and dcm2bids to structure raw biomedical imaging data into a BIDS-compliant directory layout.

What is the best way to validate a dataset against the BIDS specification?▼

Validating a dataset against the BIDS specification involves checking your organized neuroscience data for compliance using the bids-validator. This ensures your directory structure and metadata meet the required standards for downstream biomedical analysis.

How do I query BIDS datasets for specific files by subject and session?▼

Querying BIDS datasets for specific files by subject, session, task, run, or modality is handled efficiently through PyBIDS. This allows you to index and retrieve specific data points from your organized neuroscience dataset.

Can I organize raw EEG data into a BIDS-compliant directory structure?▼

Yes, you can organize raw EEG data into a BIDS-compliant directory structure. The process guides you through converting and structuring your electrophysiological data to ensure full compatibility with existing BIDS tools.

Does processing BIDS datasets require installing HeuDiConv and pydicom?▼

Yes, processing BIDS datasets requires dependencies including PyBIDS, bids-validator, HeuDiConv, dcm2bids, nibabel, and pydicom. These tools are necessary for dataset indexing, validation, DICOM conversion, and metadata management.

How do I write and edit JSON sidecar metadata files for BIDS datasets?▼

Writing and editing JSON sidecar metadata files for BIDS datasets is managed through automated metadata handling. This ensures your neuroscience data files contain the correct descriptive parameters required by the BIDS standard.

Related Skills

Explore More Education & Research Skills→
Lord1EgyptLord1Egypt
2

bids

Organize and validate neuroscience data according to the BIDS specification.

Community
Advanced
CUHK-AIM-GroupCUHK-AIM-Group
78

brain-visualization

Translate neuroimaging outputs into publication-ready figures and 3D meshes.

Official
Intermediate
awslabsawslabs
13

dicom-processing

Converts, organizes, and anonymizes DICOM/NIfTI medical imaging data for research workflows.

Official
Advanced
bcmcpherbcmcpher

bids

Validate and organize BIDS-compliant neuroimaging dataset structures.

Community
Advanced